diff --git a/croppa/main.py b/croppa/main.py
index 8457d51..762bbfc 100644
--- a/croppa/main.py
+++ b/croppa/main.py
@@ -1244,15 +1244,12 @@ class VideoEditor:
             
             # Only extract if we don't already have features for this frame
             if self.current_frame not in self.feature_tracker.features:
-                # Extract features from the cropped region of the original frame
-                if self.crop_rect:
-                    x, y, w, h = self.crop_rect
-                    cropped_frame = self.current_display_frame[y:y+h, x:x+w]
-                    if cropped_frame.size > 0:
-                        self.feature_tracker.extract_features(cropped_frame, self.current_frame)
-                else:
-                    # No crop - extract from full frame
-                    self.feature_tracker.extract_features(self.current_display_frame, self.current_frame)
+                # Extract features from the transformed frame (what user sees)
+                # 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:
+                    # Extract features without coordinate mapping - store in transformed frame coordinates
+                    self.feature_tracker.extract_features(display_frame, self.current_frame)
 
     def jump_to_previous_marker(self):
         """Jump to the previous tracking marker (frame with tracking points)."""
@@ -1518,15 +1515,11 @@ class VideoEditor:
         if self.feature_tracker.tracking_enabled:
             feature_pos = self.feature_tracker.get_tracking_position(frame_number)
             if feature_pos:
-                # Features are in cropped coordinate space, need to map to original frame coordinates
-                if self.crop_rect:
-                    crop_x, crop_y, crop_w, crop_h = self.crop_rect
-                    # Map from cropped coordinates to original frame coordinates
-                    orig_x = feature_pos[0] + crop_x
-                    orig_y = feature_pos[1] + crop_y
-                else:
-                    # No crop - coordinates are already in original frame space
-                    orig_x, orig_y = feature_pos[0], feature_pos[1]
+                # Features are stored in transformed frame coordinates
+                # We need to map them to rotated frame coordinates for the tracking system
+                # The transformed frame coordinates are already in the correct space for display
+                # But we need to map them back to the original frame space first
+                orig_x, orig_y = self._map_transformed_to_original_coords(feature_pos[0], feature_pos[1])
                 
                 # Transform to rotated frame coordinates
                 rot_x, rot_y = self._map_original_to_rotated_coords(orig_x, orig_y)
@@ -2314,17 +2307,10 @@ class VideoEditor:
             self.current_frame in self.feature_tracker.features):
             feature_positions = self.feature_tracker.features[self.current_frame]['positions']
             for (fx, fy) in feature_positions:
-                # Features are in cropped coordinate space, need to map to original frame coordinates
-                if self.crop_rect:
-                    crop_x, crop_y, crop_w, crop_h = self.crop_rect
-                    # Map from cropped coordinates to original frame coordinates
-                    orig_x = fx + crop_x
-                    orig_y = fy + crop_y
-                else:
-                    # No crop - coordinates are already in original frame space
-                    orig_x, orig_y = fx, fy
-                
-                # Convert from original frame coordinates to rotated frame coordinates
+                # Features are stored in transformed frame coordinates
+                # We need to map them to screen coordinates for display
+                # The transformed frame coordinates need to be mapped to rotated frame coordinates first
+                orig_x, orig_y = self._map_transformed_to_original_coords(fx, fy)
                 rot_x, rot_y = self._map_original_to_rotated_coords(orig_x, orig_y)
                 sx, sy = self._map_rotated_to_screen(rot_x, rot_y)
                 cv2.circle(canvas, (sx, sy), 4, (0, 255, 0), -1)  # Green circles for features
@@ -3577,28 +3563,19 @@ class VideoEditor:
             elif key == ord("T"):
                 # Extract features from current frame (Shift+T)
                 if not self.is_image_mode and self.current_display_frame is not None:
-                    # Extract features from the cropped region of the original frame
-                    # This gives us features only from the visible area with correct coordinates
-                    if self.crop_rect:
-                        x, y, w, h = self.crop_rect
-                        cropped_frame = self.current_display_frame[y:y+h, x:x+w]
-                        if cropped_frame.size > 0:
-                            success = self.feature_tracker.extract_features(cropped_frame, self.current_frame)
-                            if success:
-                                count = self.feature_tracker.get_feature_count(self.current_frame)
-                                self.show_feedback_message(f"Extracted {count} features from crop area")
-                            else:
-                                self.show_feedback_message("Failed to extract features")
-                        else:
-                            self.show_feedback_message("Crop area too small")
-                    else:
-                        # No crop - extract from full frame
-                        success = self.feature_tracker.extract_features(self.current_display_frame, self.current_frame)
+                    # Extract features from the transformed frame (what user sees)
+                    # 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:
+                        # Extract features without coordinate mapping - store in transformed frame coordinates
+                        success = self.feature_tracker.extract_features(display_frame, self.current_frame)
                         if success:
                             count = self.feature_tracker.get_feature_count(self.current_frame)
-                            self.show_feedback_message(f"Extracted {count} features from full frame")
+                            self.show_feedback_message(f"Extracted {count} features from visible area")
                         else:
                             self.show_feedback_message("Failed to extract features")
+                    else:
+                        self.show_feedback_message("No display frame available")
                     self.save_state()
                 else:
                     self.show_feedback_message("No frame data available")