I am trying to use gf on a file path with parenthesis like below
$(env_var)/aaa/bbb/foo.txt
Even though I set isfname but it seems Vim takes it as a whitespace
set isfname -=(,)
When I used isfname like below, it seems parentheses are read by Vim but it doesn't work
set isfname +=(,)
Is there any way to use gf with env var inside of parenthesis?
To do more sophisticated substitutions on gf, you can use includeexpr. It provides a fallback for gf as documented in :help gf.
First, you need to add parentheses to isfname as you have already done to capture $(env_var)
Then you can write a tiny, substituting function.
To use it only on makefiles, you can put the following code in ~/.vim/after/ftplugin/make.vim:
setlocal isfname+=(,)
setlocal includeexpr=substitute(v:fname,'\\$(\\(.\\{-}\\))','\\=getenv(submatch(1))','g')
This will look through the file name below the cursor and replace the string $(env_var) with the result of getenv(env_var). The regular expression looks a bit intimidating because backslashes have to be escaped twice. It is roughly equivalent to $(.*) and captures anything inside the parentheses non-greedily as a submatch. That submatch is then fed into getenv().
See :help 'includeexpr' and :help substitute() for reference.
For Vim to source a filetype plugin, you will also need to set (at least) :filetype plugin on as explained in :help :filetype-plugin-on.
Keep in mind that env_var may have a completely different value when you're editing and when you're running your file.
A more orthodox alternative would be to add wherever env_var points to to the path option. See :help 'path'.