EDIT: Beaten to the punch by Towerguy, with a very similar approach. :-)
If I understand your question, you have a video file (recorded with Camtasia, presumably) of a drawing being progressively drawn. The cursor position is represented throughout that video as a yellow circle.
You can seperate the yellow cursor indicator with keying. My approach would be:
Put a white solid layer below your footage layer.
Apply a Linear Colour Key to the footage, and sample the yellow colour. Adjust settings until the yellow cleanly disappears.
Duplicate the footage layer. Create a new solid layer that is the colour you want the cursor to be - maybe the same yellow, maybe another colour. Place this solid layer below the uppermost footage layer.
Set the Track Matte option on the new colour solid to "Alpha Inverted Matte".
Precompose the new color solid and upper footage layer (if you want to keep things tidy).
Now you have a cursor layer and the footage layer, independent of each other.
You could also motion track the yellow cursor and then replace the cursor entirely with whatever indicator graphic or shape you wanted.
