Hmm. I not sure what you're doing or how you're doing it but I'll give it a shot. I'm not sure if you can mask an externally loaded file, but you do have a lot of control over it if you import it into empty movie clip:
First, be sure to create an empty movie clip on your stage, it can be just a tiny black box, and give it an instance name, for example, mcHolder for movie clip SWF holder.
Next use the Load Movie command to load the external SWF, for example:
loadMovie("PNGimage.SWF", "mcHolder");
The above command loads the external movie into the mcHolder movie clip. From there, you have a lot of control over the mcHolder. You can move it places on the stage, change its visibility from visible to invisible, adjust its alpha state, start and stop the playing, determine the number of frames in it. (Maybe even mask it. But I've never tried that.) You do these things using the onClipEvent command. Look it up in online help.
I learned how to do this stuff by using the Flash MX Bible. It's kind of daunting in its scope but it covers control of external movies clips really well. Plus the CD in back allows you to copy existing movies and modify them to your needs. Pricey, so you make the call on if its worth it.
Hope this helps.
Kesey Seven