With Family Tree Maker 6, the only version I have any experience with, when you go to the FILE menu and select "Copy/Export Family File" and you get the "New Family File" dialogue window, you have a choice of six formats to save the data in, two are GEDCOM (*.GED) files. I don't know if there is any difference in the two or not, but for export to another program I always choose the one that doesn't mention FTM. The remaining file formats are for differing versions of Family Tree Maker.
PAF will not work with anything but the GED file extension from FTM!
You can also export part of a database by selecting a tree view and using the file menu to export individuals in the tree.
FTM also changes the file association for files with the GED extension to itself.This is a Windows setting that you can alter (after getting rid of FTM if that is what you plan to do) by: Click on the Start button, Select "Settings" Select "Folder options" Choose the"File types" tab Scroll down untill you find the files with a GED extension, (probably under FTW GEDCOM File, FTM , as you said, has to have things it's way) Now click on EDIT, You can change a lot of things about it here Check in the large box at the bottom, when you highlight soemthing in there and click on EDIT you can change which program does what withthe file. FTM will change the association back to itself if it is ever run again.