This happens to me all the time, I command+shift+4 to get a crosshair cursor on mac and then I can draw any shape I want. But trying to get a perfect 50x50 or 100x100 is very hard. I end up with 52x49 or 101x103. I know there is snagit from techsmith but is there anything free that does this?
The CLI also is an option for some use cases. See man screencapture.