If you know the file name, select that which applies:
cached file: use the Flush Cache command to get rid of it
local file: use the Delete Files command to get rid of it
FS BTree: you must Scavenge. You will likely loose a few attachments from your name space.
VM Backing File: use the Create VM Backing command twice: once to shrink the file to free the page, and after the "Regain Consistency" step below, use Create VM Backing again to set the backing file to the proper size.
Root Files: (Checkpoint, Boot, Cedar Microcode, ...): use the Delete Checkpoint (or whatever) command in ExtraIago.