The letters in STAM “hang” below the line (unlike most writing we are familiar with, where the letters “sit” on top of the line). The lines – called sirtut – are scored into the klaf with a steel awl. In Sifrei Torah, Megilos, Nevi’im and Mezuzos (but not Tefilin), there is a requirement that every letter must be written on sirtut. If the sirtut for 3 letters is erased (or otherwise missing), the Sefer or Mezuza is pasul according to many opinions. There is a disagreement among the Poskim if the sirtut can be put in (or put back in) after the writing already exists. Tefilin just need sirtut for the outer margins, but the custom is to put sirtut on all the lines of Tefilin as well – just to keep the writing straight.
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STAM 101 introduction & index
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More about sirtut