diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7bcc18f8..11fe5c6a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -54,6 +54,7 @@ jobs:
 
   # Tests with pytest
   tests:
+    timeout-minutes: 15
     strategy:
       fail-fast: false
       matrix:
diff --git a/sleap_io/__init__.py b/sleap_io/__init__.py
index 9e63e48b..a872bf00 100644
--- a/sleap_io/__init__.py
+++ b/sleap_io/__init__.py
@@ -26,4 +26,5 @@
     save_jabs,
     load_video,
     load_file,
+    save_file,
 )
diff --git a/sleap_io/model/labeled_frame.py b/sleap_io/model/labeled_frame.py
index c771d49f..be7b957b 100644
--- a/sleap_io/model/labeled_frame.py
+++ b/sleap_io/model/labeled_frame.py
@@ -104,3 +104,11 @@ def unused_predictions(self) -> list[Instance]:
             ]
 
         return unused_predictions
+
+    def remove_predictions(self):
+        """Remove all `PredictedInstance` objects from the frame."""
+        self.instances = [inst for inst in self.instances if type(inst) == Instance]
+
+    def remove_empty_instances(self):
+        """Remove all instances with no visible points."""
+        self.instances = [inst for inst in self.instances if not inst.is_empty]
diff --git a/sleap_io/model/labels.py b/sleap_io/model/labels.py
index f3581ceb..0419a5db 100644
--- a/sleap_io/model/labels.py
+++ b/sleap_io/model/labels.py
@@ -63,6 +63,27 @@ def __getitem__(self, key: int) -> list[LabeledFrame] | LabeledFrame:
         """Return one or more labeled frames based on indexing criteria."""
         if type(key) == int:
             return self.labeled_frames[key]
+        elif type(key) == slice:
+            return [self.labeled_frames[i] for i in range(*key.indices(len(self)))]
+        elif type(key) == list:
+            return [self.labeled_frames[i] for i in key]
+        elif isinstance(key, np.ndarray):
+            return [self.labeled_frames[i] for i in key.tolist()]
+        elif type(key) == tuple and len(key) == 2:
+            video, frame_idx = key
+            res = self.find(video, frame_idx)
+            if len(res) == 1:
+                return res[0]
+            elif len(res) == 0:
+                raise IndexError(
+                    f"No labeled frames found for video {video} and "
+                    f"frame index {frame_idx}."
+                )
+        elif type(key) == Video:
+            res = self.find(key)
+            if len(res) == 0:
+                raise IndexError(f"No labeled frames found for video {key}.")
+            return res
         else:
             raise IndexError(f"Invalid indexing argument for labels: {key}")
 
@@ -248,3 +269,99 @@ def find(
                 results.append(LabeledFrame(video=video, frame_idx=frame_ind))
 
         return results
+
+    def save(self, filename: str, format: Optional[str] = None, **kwargs):
+        """Save labels to file in specified format.
+
+        Args:
+            filename: Path to save labels to.
+            format: The format to save the labels in. If `None`, the format will be
+                inferred from the file extension. Available formats are "slp", "nwb",
+                "labelstudio", and "jabs".
+        """
+        from sleap_io import save_file
+
+        save_file(self, filename, format=format, **kwargs)
+
+    def clean(
+        self,
+        frames: bool = True,
+        empty_instances: bool = False,
+        skeletons: bool = True,
+        tracks: bool = True,
+        videos: bool = False,
+    ):
+        """Remove empty frames, unused skeletons, tracks and videos.
+
+        Args:
+            frames: If `True` (the default), remove empty frames.
+            empty_instances: If `True` (NOT default), remove instances that have no
+                visible points.
+            skeletons: If `True` (the default), remove unused skeletons.
+            tracks: If `True` (the default), remove unused tracks.
+            videos: If `True` (NOT default), remove videos that have no labeled frames.
+        """
+        used_skeletons = []
+        used_tracks = []
+        used_videos = []
+        kept_frames = []
+        for lf in self.labeled_frames:
+
+            if empty_instances:
+                lf.remove_empty_instances()
+
+            if frames and len(lf) == 0:
+                continue
+
+            if videos and lf.video not in used_videos:
+                used_videos.append(lf.video)
+
+            if skeletons or tracks:
+                for inst in lf:
+                    if skeletons and inst.skeleton not in used_skeletons:
+                        used_skeletons.append(inst.skeleton)
+                    if (
+                        tracks
+                        and inst.track is not None
+                        and inst.track not in used_tracks
+                    ):
+                        used_tracks.append(inst.track)
+
+            if frames:
+                kept_frames.append(lf)
+
+        if videos:
+            self.videos = [video for video in self.videos if video in used_videos]
+
+        if skeletons:
+            self.skeletons = [
+                skeleton for skeleton in self.skeletons if skeleton in used_skeletons
+            ]
+
+        if tracks:
+            self.tracks = [track for track in self.tracks if track in used_tracks]
+
+        if frames:
+            self.labeled_frames = kept_frames
+
+    def remove_predictions(self, clean: bool = True):
+        """Remove all predicted instances from the labels.
+
+        Args:
+            clean: If `True` (the default), also remove any empty frames and unused
+                tracks and skeletons. It does NOT remove videos that have no labeled
+                frames or instances with no visible points.
+
+        See also: `Labels.clean`
+        """
+        for lf in self.labeled_frames:
+            lf.remove_predictions()
+
+        if clean:
+            self.clean(
+                frames=True,
+                empty_instances=False,
+                skeletons=True,
+                tracks=True,
+                videos=False,
+            )
diff --git a/tests/model/test_labeled_frame.py b/tests/model/test_labeled_frame.py
index f8093ced..b542124e 100644
--- a/tests/model/test_labeled_frame.py
+++ b/tests/model/test_labeled_frame.py
@@ -3,6 +3,7 @@
 from numpy.testing import assert_equal
 from sleap_io import Video, Skeleton, Instance, PredictedInstance
 from sleap_io.model.labeled_frame import LabeledFrame
+import numpy as np
 
 
 def test_labeled_frame():
@@ -26,3 +27,51 @@ def test_labeled_frame():
 
     # Test LabeledFrame.__getitem__ method
     assert lf[0] == inst
+
+
+def test_remove_predictions():
+    """Test removing predictions from `LabeledFrame`."""
+    inst = Instance([[0, 1], [2, 3]], skeleton=Skeleton(["A", "B"]))
+    lf = LabeledFrame(
+        video=Video(filename="test"),
+        frame_idx=0,
+        instances=[
+            inst,
+            PredictedInstance([[4, 5], [6, 7]], skeleton=Skeleton(["A", "B"])),
+        ],
+    )
+
+    assert len(lf) == 2
+    assert len(lf.predicted_instances) == 1
+
+    # Remove predictions
+    lf.remove_predictions()
+
+    assert len(lf) == 1
+    assert len(lf.predicted_instances) == 0
+    assert type(lf[0]) == Instance
+    assert_equal(lf.numpy(), [[[0, 1], [2, 3]]])
+
+
+def test_remove_empty_instances():
+    """Test removing empty instances from `LabeledFrame`."""
+    inst = Instance([[0, 1], [2, 3]], skeleton=Skeleton(["A", "B"]))
+    lf = LabeledFrame(
+        video=Video(filename="test"),
+        frame_idx=0,
+        instances=[
+            inst,
+            Instance(
+                [[np.nan, np.nan], [np.nan, np.nan]], skeleton=Skeleton(["A", "B"])
+            ),
+        ],
+    )
+
+    assert len(lf) == 2
+
+    # Remove empty instances
+    lf.remove_empty_instances()
+
+    assert len(lf) == 1
+    assert type(lf[0]) == Instance
+    assert_equal(lf.numpy(), [[[0, 1], [2, 3]]])
diff --git a/tests/model/test_labels.py b/tests/model/test_labels.py
index e52a8103..0060a220 100644
--- a/tests/model/test_labels.py
+++ b/tests/model/test_labels.py
@@ -8,9 +8,12 @@
     Instance,
     PredictedInstance,
     LabeledFrame,
+    Track,
     load_slp,
+    load_video,
 )
 from sleap_io.model.labels import Labels
+import numpy as np
 
 
 def test_labels():
@@ -117,3 +120,141 @@ def test_labels_skeleton():
     labels.skeletons.append(Skeleton(["B"]))
     with pytest.raises(ValueError):
         labels.skeleton
+
+
+def test_labels_getitem(slp_typical):
+    labels = load_slp(slp_typical)
+    labels.labeled_frames.append(LabeledFrame(video=labels.video, frame_idx=1))
+    assert len(labels) == 2
+    assert labels[0].frame_idx == 0
+    assert len(labels[:2]) == 2
+    assert len(labels[[0, 1]]) == 2
+    assert len(labels[np.array([0, 1])]) == 2
+    assert labels[(labels.video, 0)].frame_idx == 0
+
+    with pytest.raises(IndexError):
+        labels[(labels.video, 2000)]
+
+    assert len(labels[labels.video]) == 2
+
+    with pytest.raises(IndexError):
+        labels[Video(filename="test")]
+
+    with pytest.raises(IndexError):
+        labels[None]
+
+
+def test_labels_save(tmp_path, slp_typical):
+    labels = load_slp(slp_typical)
+    labels.save(tmp_path / "test.slp")
+    assert (tmp_path / "test.slp").exists()
+
+
+def test_labels_clean_unchanged(slp_real_data):
+    labels = load_slp(slp_real_data)
+    assert len(labels) == 10
+    assert labels[0].frame_idx == 0
+    assert len(labels[0]) == 2
+    assert labels[1].frame_idx == 990
+    assert len(labels[1]) == 2
+    assert len(labels.skeletons) == 1
+    assert len(labels.videos) == 1
+    assert len(labels.tracks) == 0
+    labels.clean(
+        frames=True, empty_instances=True, skeletons=True, tracks=True, videos=True
+    )
+    assert len(labels) == 10
+    assert labels[0].frame_idx == 0
+    assert len(labels[0]) == 2
+    assert labels[1].frame_idx == 990
+    assert len(labels[1]) == 2
+    assert len(labels.skeletons) == 1
+    assert len(labels.videos) == 1
+    assert len(labels.tracks) == 0
+
+
+def test_labels_clean_frames(slp_real_data):
+    labels = load_slp(slp_real_data)
+    assert labels[0].frame_idx == 0
+    assert len(labels[0]) == 2
+    labels[0].instances = []
+    labels.clean(
+        frames=True, empty_instances=False, skeletons=False, tracks=False, videos=False
+    )
+    assert len(labels) == 9
+    assert labels[0].frame_idx == 990
+    assert len(labels[0]) == 2
+
+
+def test_labels_clean_empty_instances(slp_real_data):
+    labels = load_slp(slp_real_data)
+    assert labels[0].frame_idx == 0
+    assert len(labels[0]) == 2
+    labels[0].instances = [
+        Instance.from_numpy(
+            np.full((len(labels.skeleton), 2), np.nan), skeleton=labels.skeleton
+        )
+    ]
+    labels.clean(
+        frames=False, empty_instances=True, skeletons=False, tracks=False, videos=False
+    )
+    assert len(labels) == 10
+    assert labels[0].frame_idx == 0
+    assert len(labels[0]) == 0
+
+    labels.clean(
+        frames=True, empty_instances=True, skeletons=False, tracks=False, videos=False
+    )
+    assert len(labels) == 9
+
+
+def test_labels_clean_skeletons(slp_real_data):
+    labels = load_slp(slp_real_data)
+    labels.skeletons.append(Skeleton(["A", "B"]))
+    assert len(labels.skeletons) == 2
+    labels.clean(
+        frames=False, empty_instances=False, skeletons=True, tracks=False, videos=False
+    )
+    assert len(labels) == 10
+    assert len(labels.skeletons) == 1
+
+
+def test_labels_clean_tracks(slp_real_data):
+    labels = load_slp(slp_real_data)
+    labels.tracks.append(Track(name="test1"))
+    labels.tracks.append(Track(name="test2"))
+    assert len(labels.tracks) == 2
+    labels[0].instances[0].track = labels.tracks[1]
+    labels.clean(
+        frames=False, empty_instances=False, skeletons=False, tracks=True, videos=False
+    )
+    assert len(labels) == 10
+    assert len(labels.tracks) == 1
+    assert labels[0].instances[0].track == labels.tracks[0]
+    assert labels.tracks[0].name == "test2"
+
+
+def test_labels_clean_videos(slp_real_data):
+    labels = load_slp(slp_real_data)
+    labels.videos.append(Video(filename="test2"))
+    assert len(labels.videos) == 2
+    labels.clean(
+        frames=False, empty_instances=False, skeletons=False, tracks=False, videos=True
+    )
+    assert len(labels) == 10
+    assert len(labels.videos) == 1
+    assert labels.video.filename == "tests/data/videos/centered_pair_low_quality.mp4"
+
+
+def test_labels_remove_predictions(slp_real_data):
+    labels = load_slp(slp_real_data)
+    assert len(labels) == 10
+    assert sum([len(lf.predicted_instances) for lf in labels]) == 12
+    labels.remove_predictions(clean=False)
+    assert len(labels) == 10
+    assert sum([len(lf.predicted_instances) for lf in labels]) == 0
+
+    labels = load_slp(slp_real_data)
+    labels.remove_predictions(clean=True)
+    assert len(labels) == 5
+    assert sum([len(lf.predicted_instances) for lf in labels]) == 0