The traditional way to do this is by putting the keys you have to check repeatedly in a hash-variable which is very fast to look-up, even when there are many items to look-up. Then you can read the other file line by line and check the keys.

Rather than using a regex to extract the keys, the following example uses split

use Modern::Perl;

open my $NAMES, '<', './file2.txt' or die 'Could not open file2.txt';
my %names;
while (<$NAMES>) {
    chomp;
    next unless $_;
    $names{(split)[2]}=1;
}
close $NAMES;

open my $DATA, '<', './file1.txt' or die 'Could not open file1.txt';
while (<$DATA>) {
    chomp;
    next unless $_;
    say unless $names{(split)[1]};
}
close $DATA;
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Output:

ID alan135/xkr $work(b05bfn00un0c3)/b05bfn00un0c3 ; #<= b05bfn00un0d0 
+Size:5848.270996
ID sam012/pp $work(b05bfn00ld0p7)/b05bfn00ld0p7 ; #<= b05bfn00ld0s0 Si
+ze:INFINITY
ID Steve9018 $work(b05bfn00ld0p7)/b05bfn00ld0p7 ; #<= b05bfn00ld0s0 Si
+ze:INFINITY
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