Removable switches (per
@CountMike) is likely to be the most viable option.
Even if the key caps are removed, the switch stems will probably extend above the surface of the keyboard.
So you would need to remove the switches leaving just the openings.
And I would expect that the openings could be covered in some manner for the sake of appearance and to keep out debris.
= = = =
That said, I would be remiss if I did not ask about "and some of those have keys in strange places that I don't want/will use."
What is preventing you from simply ignoring those keys? Is there a concern that some end user or you could accidentally press those keys? Is it the cosmetics?
Curious about the project but not asking per se.
Plus, things being as they often are, you may later discover that those keys will be needed again....
Mr. Murphy loves projects.
In any case, you could (as mentioned) use code to disable the keys. Which offers the advantage of being able to undo or change key actions very easily.
Consider that if something is not working then you can be fairly certain that the keyboard "mods" etc. are not the issue.
My suggestion is to simply get the project working first.
Then deal with keys, keyboards, cosmetics, etc. later on - If and when necessary.