File1 has three columns
Really? Your first line is: 
Box of Joe     CA12DE    12345

[download]
Why is that three columns, not five?

For the rest of the post, I will assume your columns are tab separated. (Maybe your data actually does contain tabs, but I cannot see that). Adjust accordingly if columns are defined differently. Either use a hash, or ~~ (untested): 

chomp(my @file2 = <F2>);
while (<F1>) {
    print unless @file2 ~~ (split /\t/)[1];
}

[download]
See also the questions "How can I tell whether a certain element is contained in a list or array?", "How can I remove duplicate elements from a list or array?", and "How do I compute the difference of two arrays? How do I compute the intersection of two arrays?" from the perlfaq. (man perlfaq4).

In reply to Re: comparing columns using regular expression by JavaFan
in thread comparing columns using regular expression by rocky13

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