You will need to use a custom mapping or override the default FuzzyFinder mapping to run it. There you can check the open NERDTree and go to the previous window (or maybe close NERDTree), for example:
:nnoremap <silent> <F5> :<Cu>if exists("t:NERDTreeBufName") && bufwinnr(t:NERDTreeBufName) == winnr() <Bar> wincmd p <Bar> endif <Bar> FufBuffer<CR>
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