With a regular expression and a well placed map your nested loop can be reduced to a single line

## build a regular expression to match all the words in @ignore
my $ignore = '(?:\b'. join('\b|\b', map quotemeta, @ignore). '\b)';

## assuming @words contains the contents of the file
s/$ignore// for map lc, @words;
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Now it's just a matter of writing @words back to the original file. See. quotemeta, join, map and lc for info on the functions used in the above snippet, perlsyn for info on the for modifier and perlre for further details of the regex used.
HTH

_________
broquaint

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