Putting the extensions in another array (but kinda ugly):

my @exts;
my @eFILES = grep { 
    /^env\.([a-z]{3})$/; push @exts, $1 if $1 
    && ($_ ne 'env.fix') 
    && -f "$LIBDIR/$_"
} readdir(LDIR);
[download]

Note that your 1st regex is not needed ((!/^\./)) because you are also checking for env at the start of the string.

Updated to make a little more readable.