It depends how you do the backup in the first place.
If you backup all your files from your PC into one big compressed file on the external hard drive (like using an actual backup program), then no, you cannot delete files from your main drive because you wont be able to restore the files one by one.
The best way to do what you want is to simply drag the files you want off of your main pc onto the external drive in an explorer window.
Confirm they are actually on the external drive, then you can delete the file from you main pc to make room.
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