diff --git a/croppa/main.py b/croppa/main.py
index 1a70998..a8fc325 100644
--- a/croppa/main.py
+++ b/croppa/main.py
@@ -1248,9 +1248,21 @@ class VideoEditor:
                 # This handles all transformations (crop, zoom, rotation) correctly
                 display_frame = self.apply_crop_zoom_and_rotation(self.current_display_frame)
                 if display_frame is not None:
-                    # Store features in rotated frame coordinates (like existing motion tracking)
+                    # Map coordinates from transformed frame to rotated frame coordinates
+                    # Use the existing coordinate transformation system
                     def coord_mapper(x, y):
-                        return (int(x), int(y))
+                        # Map from transformed frame coordinates to screen coordinates
+                        frame_height, frame_width = display_frame.shape[:2]
+                        available_height = self.window_height - (0 if self.is_image_mode else self.TIMELINE_HEIGHT)
+                        start_y = (available_height - frame_height) // 2
+                        start_x = (self.window_width - frame_width) // 2
+                        
+                        # Convert to screen coordinates
+                        screen_x = x + start_x
+                        screen_y = y + start_y
+                        
+                        # Use the existing coordinate transformation system
+                        return self._map_screen_to_rotated(screen_x, screen_y)
                     
                     self.feature_tracker.extract_features(display_frame, self.current_frame, coord_mapper)
 
@@ -2676,6 +2688,9 @@ class VideoEditor:
         self.tracking_enabled = False
         self.tracking_points = {}
         
+        # Reset feature tracking
+        self.feature_tracker.clear_features()
+        
         # Reset cut markers
         self.cut_start_frame = None
         self.cut_end_frame = None
@@ -3561,13 +3576,26 @@ class VideoEditor:
                     # This handles all transformations (crop, zoom, rotation) correctly
                     display_frame = self.apply_crop_zoom_and_rotation(self.current_display_frame)
                     if display_frame is not None:
-                        # Store features in rotated frame coordinates (like existing motion tracking)
-                        # This way we can reuse the existing display system
+                        # Map coordinates from transformed frame to rotated frame coordinates
+                        # Use the existing coordinate transformation system
                         def coord_mapper(x, y):
-                            # The transformed frame coordinates are already in the right space
-                            # We just need to map them to rotated frame coordinates
-                            # Since the transformed frame is what the user sees, we can use it directly
-                            return (int(x), int(y))
+                            # The transformed frame coordinates are in the display frame space
+                            # We need to map them to screen coordinates first, then use the existing
+                            # _map_screen_to_rotated function
+                            
+                            # Map from transformed frame coordinates to screen coordinates
+                            # The transformed frame is centered on the canvas
+                            frame_height, frame_width = display_frame.shape[:2]
+                            available_height = self.window_height - (0 if self.is_image_mode else self.TIMELINE_HEIGHT)
+                            start_y = (available_height - frame_height) // 2
+                            start_x = (self.window_width - frame_width) // 2
+                            
+                            # Convert to screen coordinates
+                            screen_x = x + start_x
+                            screen_y = y + start_y
+                            
+                            # Use the existing coordinate transformation system
+                            return self._map_screen_to_rotated(screen_x, screen_y)
                         
                         success = self.feature_tracker.extract_features(display_frame, self.current_frame, coord_mapper)
                         if success: