After the sofer writes the Torah passages, a qualified proof-reader - one with expert knowledge in the laws of Biblical text-writing - reviews every letter of the text. He must also be capable of finding solutions to any problems he may discover in the writing.
There are several stages in proofreading:
First, he checks for missing, extra, or mistaken letters.
Second, he checks to make sure that each letter has the required tagim (crownlets).
Third, the paragraphs and the lines (p'tuchot and s'tumot) is checked, to ensure that they comply with tradition.
After all this, the texts are reviewed yet again by computer.