diff --git a/python/lsst/ts/externalscripts/auxtel/latiss_take_twilight_flats.py b/python/lsst/ts/externalscripts/auxtel/latiss_take_twilight_flats.py
index 26d1558af..a9022f728 100644
--- a/python/lsst/ts/externalscripts/auxtel/latiss_take_twilight_flats.py
+++ b/python/lsst/ts/externalscripts/auxtel/latiss_take_twilight_flats.py
@@ -209,3 +209,15 @@ async def slew_azel_and_setup_instrument(self, az, el):
             filter=self.config.filter,
             grating=self.config.grating,
         )
+
+    async def setup_instrument(self, az, el):
+        """Abstract method to set the instrument. Change the filter
+        and start tracking.
+        """
+        # slew to desired field
+        await self.tcs.start_tracking()
+
+        await self.latiss.setup_instrument(
+            filter=self.config.filter,
+            grating=self.config.grating,
+        )
diff --git a/python/lsst/ts/externalscripts/base_take_twilight_flats.py b/python/lsst/ts/externalscripts/base_take_twilight_flats.py
index 66a39680a..a735e65b8 100644
--- a/python/lsst/ts/externalscripts/base_take_twilight_flats.py
+++ b/python/lsst/ts/externalscripts/base_take_twilight_flats.py
@@ -177,6 +177,13 @@ async def slew_azel_and_setup_instrument(self, az, el):
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
+    async def setup_instrument(self):
+        """Abstract method to set the instrument. Change the filter
+        and slew and track target.
+        """
+        raise NotImplementedError()
+
     @classmethod
     def get_schema(cls):
         schema_yaml = """
@@ -242,6 +249,11 @@ def get_schema(cls):
                 description: If True, track sky. If False, keep az and el constant.
                 type: boolean
                 default: True
+              position_telescope:
+                description: If True, position telescope relative to the sun. \
+                    If False, assume the telescope is in correct position.
+                type: boolean
+                default: True
               ignore:
                 description: >-
                     CSCs from the camera group to ignore in status check.
@@ -249,7 +261,6 @@ def get_schema(cls):
                 type: array
                 items:
                   type: string
-
             additionalProperties: false
         """
         schema_dict = yaml.safe_load(schema_yaml)
@@ -282,10 +293,13 @@ async def configure(self, config: types.SimpleNamespace):
                 if comp in self.camera.components_attr:
                     self.log.debug(f"Ignoring Camera component {comp}.")
                     setattr(self.camera.check, comp, False)
+                elif comp in self.tcs.components_attr:
+                    self.log.debug(f"Ignoring component {comp}.")
+                    setattr(self.tcs.check, comp, False)
                 else:
                     self.log.warning(
                         f"Component {comp} not in CSC Group. "
-                        f"Must be one of {self.camera.components_attr}. "
+                        f"Must be one of {self.camera.components_attr} or  {self.tcs.components_attr}."
                         f"Ignoring."
                     )
 
@@ -465,16 +479,19 @@ async def take_twilight_flats(self):
         # get an empty field
         search_area_degrees = 0.05
 
-        if self.config.tracking:
-            ra, dec = await self.get_twilight_flat_sky_coords(
-                target, radius=search_area_degrees
-            )
+        if self.config.position_telescope:
+            if self.config.tracking:
+                ra, dec = await self.get_twilight_flat_sky_coords(
+                    target, radius=search_area_degrees
+                )
 
-            await self.track_radec_and_setup_instrument(ra, dec)
-        else:
-            az = self.get_target_az()
+                await self.track_radec_and_setup_instrument(ra, dec)
+            else:
+                az = self.get_target_az()
 
-            await self.slew_azel_and_setup_instrument(az, self.config.target_el)
+                await self.slew_azel_and_setup_instrument(az, self.config.target_el)
+        else:
+            await self.setup_instrument()
 
         # Take one 1s flat to calibrate the exposure time
         self.log.info("Taking 1s flat to calibrate exposure time.")
diff --git a/python/lsst/ts/externalscripts/maintel/take_twilight_flats_comcam.py b/python/lsst/ts/externalscripts/maintel/take_twilight_flats_comcam.py
index a5fe698f5..653854227 100644
--- a/python/lsst/ts/externalscripts/maintel/take_twilight_flats_comcam.py
+++ b/python/lsst/ts/externalscripts/maintel/take_twilight_flats_comcam.py
@@ -227,6 +227,24 @@ async def slew_azel_and_setup_instrument(self, az, el):
             el=el,
         )
 
+    async def setup_instrument(self):
+        """Abstract method to set the instrument. Change the filter
+        and track target.
+        """
+        current_filter = await self.comcam.get_current_filter()
+
+        if current_filter != self.config.filter:
+            self.log.debug(
+                f"Filter change required: {current_filter} -> {self.config.filter}"
+            )
+            await self.comcam.setup_filter(filter=self.config.filter)
+        else:
+            self.log.debug(
+                f"Already in the desired filter ({current_filter}). Starting tracking"
+            )
+
+        await self.mtcs.start_tracking()
+
     async def configure(self, config):
         """Take the sequence of twilight flats twilight flats."""
         self.configure_client()
diff --git a/python/lsst/ts/externalscripts/maintel/take_twilight_flats_lsstcam.py b/python/lsst/ts/externalscripts/maintel/take_twilight_flats_lsstcam.py
index bc72f7c41..fede31e47 100644
--- a/python/lsst/ts/externalscripts/maintel/take_twilight_flats_lsstcam.py
+++ b/python/lsst/ts/externalscripts/maintel/take_twilight_flats_lsstcam.py
@@ -223,3 +223,21 @@ async def slew_azel_and_setup_instrument(self, az, el):
             az=az,
             el=el,
         )
+
+    async def setup_instrument(self):
+        """Abstract method to set the instrument. Change the filter
+        and slew and track target.
+        """
+        current_filter = await self.lsstcam.get_current_filter()
+
+        if current_filter != self.config.filter:
+            self.log.debug(
+                f"Filter change required: {current_filter} -> {self.config.filter}"
+            )
+            await self.lsstcam.setup_filter(filter=self.config.filter)
+        else:
+            self.log.debug(
+                f"Already in the desired filter ({current_filter}), slewing."
+            )
+
+        await self.mtcs.start_tracking()