Do you mean something like this?

my @loads_of_stuff;
while ( my $line = <DATA> ) {
    chomp $line;
    while ( $line =~ m/#input(.+?)#end/g ) {
        push @loads_of_stuff, $1;
    }
}
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This will run into trouble if #input and #end are potentially on different lines in the file. If that's a possibility, you my need the range operator, or to slurp chunksof the file, or even to set the file input record separator to #end.

You will run into additional trouble if #input and #end are legal characters if placed within quotes, ie, #input "this is what you want to capture, including #end" #end