In this particular case, you could probably do something like this (as the non-matching captures aren't defined):

#!/usr/bin/perl -l

for (qw(OTHFIL.FOO BARFIL)) {
    my ($foo) = grep defined($_), /OTHFIL\.([A-Z]{3})|([A-Z]{3})FIL/;
    print $foo;
}

__END__
FOO
BAR
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