Just based on what you are telling us, I would second this approach. I've written the following code many times:

while (<FH>) {
    s/#.*$//;
    my @args = split(' ', $_);
    next unless @args;
    ... process command ...
}
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If, however, you have any recursive syntactical elements (like begin/end grouping symbols which need to be matched), a proper parser written with Parser::RecDescent is probably in order.