When purchasing an Etrog for Succot, one must ensure that the Etrog has no holes or marks, particularly in the upper third of the Etrog, before it becomes wide. However, a hole or discoloration invalidates an Etrog only if it is visible to the naked eye, through a casual, perfunctory look. If a hole or mark is visible only through the aid of a magnifying glass or microscope, it does not disqualify the Etrog. There is a famous Halachic principle known as "Lo Nitena Torah Le’mal’acheh Ha’sharet" ("The Torah was not given to the ministering angels"), which means that the Torah’s laws do not demand anything beyond ordinary human capability. Halacha does not require enlisting the use of sophisticated instruments to determine the validity of an Etrog. When the Torah requires using an Etrog that is "Hadar" ("beautiful"), it refers to the Etrog’s appearance to the naked eye. Therefore, if a person discerns a hole or discoloration during a casual inspection, the Etrog may not be used, but otherwise, the Etrog is valid and no further inspection is required.
There are numerous other applications of this principle in several different areas of Halacha. The Tiferet Yisrael commentary to Masechet Aboda Zara (by Rabbi Yisrael Lifshitz, 1782-1861) relates that a Rabbi in his time allowed eating a certain species of fish that did not have visible scales, because scales could be seen on the fish’s skin through a magnifying glass. All the other Rabbis disputed this ruling and issued a Herem (writ of excommunication) against those who partake of this species. They argued that when the Torah required the presence of fins and scales for a fish to be kosher, it referred to fins and scales that are visible to the naked eye, and microscopic scales do not qualify.
Similarly, the Aruch Hashulhan (Rabbi Yechiel Michel Epstein of Nevarduk, 1829-1908) writes that microorganisms are not forbidden for consumption, because of the rule of "Lo Nitena Torah Le’mal’acheh Ha’sharet." He notes that scientists have identified many different microscopic creatures in the air we breathe, which we invariably swallow every time we open our mouths. Clearly, the Torah does not prohibit such creatures. Only organisms that are visible to the naked eye fall under the Torah’s kashrut restrictions. (This does not necessarily apply to the recent controversy surrounding the presence of small organisms in New York City’s water, which, at least according to some, are indeed visible to the naked eye.)
Likewise, an article that was published in the journal Ha’me’asef noted that even the smoothest slaughtering knife has nicks that could be discovered through the use of a microscope. This does not mean, of course, that there is no possibility of properly slaughtering animals for meat. Halacha requires inspecting knives normally, and there is no need to use a magnifying glass, microscope, or any advanced screening methods to check a knife.
This rule applies to determining the validity of a Sefer Torah, as well. Microscopic inspection of a Torah scroll would inevitably reveal some missing ink or tiny hole somewhere in the parchment, and if these findings were Halachically significant, there would be no kosher Sefer Torah in the world. But once again, Halacha disqualifies only those features which are visible to the naked eye. This works in the opposite direction, as well. If two letters appear to touch each other, but a magnifying glass reveals a microscopic space in between them, the Sefer Torah is invalid and must be corrected. Since the two letters appear to be touching when seen by the naked eye, the Sefer Torah is disqualified even if they appear separate through magnification.
Summary: A hole or mark on the Etrog that cannot be seen to the naked eye, and is discerned only through the use of a magnifying glass, does not disqualify the Etrog for the Misva.
