# read file1 into a %hash
... code to do that here ...

# inside a loop
while (my $line = <$file2>) {
    # read file2 line by line
    ... this was done in the loop condition above ...

    # split the $line to @fields at |

    # if the first $fields[0] exists in the %hash,
        # print the whole $line to file 3
}