Following a moving object with a mask

Has anyone out there tried to follow an object with a mask in FCP? bascially I transferred a CAD video into MOV and imported it into FCP to edit it.
NOw i have a "flickering"occuring over some of the objects in the video that I have been masking with a PSD (transparent background) of 'the whole object'.. But i have to import and insert these masks each frame.... does anyone have ANY other ideas on how to resolve this.
A friend of mine said aftereffects, but i cant imagine FCP cant do it.
Thanks ahead of time... i look forward to hearing other people's smarts- as i dont have them.
I can email sample video if there are questions.

within FCP or FCS?
if you have FCS 2 you can use Motion's Analyze Motion and Match Move functions ... tutorial here
if not you could buy Lyric's Motion Tracking Kit plugin bundle
http://www.lyric.com/fcp-plugins/tracking.htm
even better would be to try to address the root of the problem ... what's with the flickering objects?

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