Every collection that has grown for a few years holds the same font more than once. The Duplicates section of the sidebar finds them, in two kinds that are worth telling apart.

Identical files are copies: the files are byte for byte the same, so whichever of them you drop, nothing is lost. Same font, other file are files that declare one family, one style and one version but differ in their bytes — the same design in another build, hinted differently or carrying another set of tables. Which of those to keep is a decision, and the Info page of each is where to make it.

The first time a kind is picked Fontmatrix reads the font files, which takes a moment; the answer is then kept until the collection changes. Only files of exactly the same length are ever read, so a collection of thousands costs a few dozen reads. Nothing is written to the database, and no font is removed for you: the filter narrows the list, and you decide what goes.

Tools → Duplicates..., or Show Groups... in the sidebar, shows the same fonts group by group, each file with its folder, size, version and whether it is activated. Show in List selects a file's font in the main list, Open Folder opens the folder it is in, and Tick the Extra Copies ticks every identical file but one in each group, keeping the activated one where there is one.

The ticked files can then be moved to the trash with Move to Trash, which you can undo from the trash of your desktop, or only removed from the collection with Remove from Collection, which leaves the files where they are. One file of every group always stays, and an activated font is deactivated before it goes. A system font comes back into the collection at the next start as long as its file is there, so it can be moved to the trash, where its folder allows it, but not only removed; a font of a remote directory can be neither.