It is forbidden to touch the parchment of the Sefer Torah with one’s bare hands. As the Gemara discusses in Masechet Shabbat, the Sages enacted a prohibition against direct contact with the parchment, and they went so far as to say that one who touches the parchment barehanded forfeits the credit he would have received for the Misva in which he was involved. For example, if a person received an Aliya, or was reading the Torah, and in the process he touched the parchment with his bare hands, he is not credited with the Misva.
For this reason, it is customary to have a special cloth – called a “Mitpahat” – hanging alongside the Sefer Torah. Many people mistakenly think that the cloth is put there for decoration, but in truth, it serves the vital purpose of enabling people to touch the parchment in a permissible fashion. Thus, for example, one who receives an Aliya, and is required to touch the parchment as he recites the Berachot, should use this cloth so he does not touch the parchment barehanded. Likewise, when one needs to turn the scroll to the next page, he should use the cloth and not touch the parchment barehanded. As mentioned, one who performs any Misva with the Sefer Torah forfeits the reward for the Misva if he touches the parchment barehanded in the process.
It is permissible to directly touch the wooden handles of the Sifreh Torah. This prohibition applies only to the parchment.
The Maharash Vital (Rav Shemuel Vital, Damascus, 1598-1677) was of the opinion that this prohibition applies only during the reading of the Sefer Torah, or when it is being taken from the Hechal for the reading. At these times, when a special spiritual “light” emanates from the Sefer Torah, it is forbidden to touch the parchment. At other times, however, such as if one wishes to roll the Sefer Torah before the prayer services so it will be set to the right place, there is no prohibition, and one may touch the parchment with his bare hands. Although the Ben Ish Hai (Rav Yosef Haim of Baghdad, 1833-1909) accepts this ruling of Rav Shemuel Vital, Hacham Ovadia Yosef notes in his work Halichot Olam that the majority of authorities dispute this position, and forbid touching the parchment barehanded at any time. Therefore, this is forbidden even outside the context of the congregational Torah reading.
The Rama (Rav Moshe Isserles of Cracow, 1525-1572) writes that it is permissible to touch the parchment of a Megilat Ester with one’s bare hands, as long as he performs Netilat Yadayim beforehand. (Of course, no Beracha is recited on this washing.) This is, indeed, the accepted Halacha.
It is permissible to touch other sacred books – Humashim, Germariyot, etc. – even without washing, unless one’s hands are dirty, in which case one should clean them first out of respect for these sacred articles.
Summary: It is forbidden to touch the parchment of the Torah scroll with one’s bare hands at any time. Therefore, whenever one needs to touch the parchment, such as when moving the scroll or when reciting the Berachot over the reading, one should use the “Mitpahat” – the cloth hanging alongside the scroll. One may touch the parchment of a Megilat Ester with one’s bare hands, as long as he performs Netilat Yadayim beforehand.