You can replace a color or transparent region within a selection of frames or a whole animation, either with another color or with a transparent region as follows:

1. Select the frame(s) on which you want to perform the color replacement.


2. Choose Animation > Replace Color. Animation Shop will open the Replace Color dialog box.


3. Use the radio buttons in the "Replace color in" panel to specify whether you wish to perform the color replacement on all the frames in the animation or just on the selected ones.


4. Select the color to be replaced by clicking on a specific area of a frame.  The selected color will automatically appear in the "Replace" panel.  You can also make your selection by clicking the colored box in the "Replace" panel and choosing a color.  Right-clicking this box will open the Recent Colors dialog box.
   
   If instead of replacing a color you wish to fill all the transparent regions inside the selected frames, select the appropriate radio button in the same panel.  Use the Tolerance and Match Mode boxes to adjust the settings of the color replacement.


5. Select the replacement color by right clicking on a specific area of a frame.  The selected color will automatically appear in the "With" panel.  As in the previous step, you can also make your selection by clicking the colored rectangle in the "With" panel and choosing a color from the Color dialog box.  Right-clicking this box will open the Recent Colors dialog box.
   
   If instead of using a color for your replacement you wish to use a transparent opacity, select the appropriate radio button in the "With" panel.


6. Click the OK button.  Animation Shop will perform the color replacement according to the settings you selected.