put them in single 'quotationmarks'
'['%year%']' %album%
$ represents the end of a line in regular expressions. So use:
Action: Replace with regular expression
Field: _FILENAME
Regular Expression: $
Replace with: )
EDIT:
a quick test showed that this gives you .mp3) which i don't understand since I thougt there is a difference between _filenam and _filename_ext.
Anyway, that makes it even easier. Use:
Action: Replace
Field: _FILENAME
Original: .mp3
Replace with: ).mp3
EDIT2:
for opening and closing bracket in one go:
Action: Replace with regular expression
Field: _FILENAME
Regular Expression: feat(.*).(...)
Replace with: (feat$1).$2
this time not only for .mp3 but for all filetypes with three characters in the file extension, represented by .(...)