After doing a google search, I found this excellent, well sourced piece from the OU. According to the article, written by rabbi Dovid Bistricer, poskim fall on both sides of the issue.
Those in favor of using microscopes to "change" the halacha:
R' Yaakov Emden (She'ilas Yaavetz 2:124) allowed microscopes to check for insects in rice, forbidding that which can only be seen with a microscope.
R' Moshe Stern (Shut Be'er Moshe 5:16) allows the use of a microscope to see if letters which appear connected in a sefer torah are in fact so, but rejected its use to pasul the letters.
The Chazon Ish (Acc to R' SZ Aurbach in R' Y. Neuwirth's SSK (3:37)) forbids insects identified with a microscope.
R' YS Elyashiv is quoted (source needed) as forbidding insects identified with a microscope if those insects will be readily identified in the future w/o a microscope, but permits those that won't be.
Others were unable to fathom how something could be permissible to one and forbidden to another depending on whether one owned a microscope:
Tiferes Yisrael (Avoda Zara 2:7:3) says that the Torah only recognizes what can be seen by the naked eye and forbids fish where the scales are not discernable without a microscope (and would presumably permit bugs of a similar nature).
R' Shlomo Klugar (Tuv Taam Vadaas KA 2:53) rejected R' Y Enden.
R' Avraham Danzig (Binas Adam 34).
R' YM Epstein (Aruch Hashulchan 84:36)
R' Moshe Feinstein (Igros Moshe Yore Deah II 146) rejected using a microscope to check the sqareness of Tefillin.
R' Moshe Shternbuch (Teshuvos v'Hanhagos 1:628 and 3:323) invalidates stam writing where the letters appear to be touching, although a microscopic view has them separated. He quotes the Tschbeiner Rav (Dovev Meisharim (1:1) as having the same position.
Rav Shmuel Vosner (Shut Shevet haLevi 7:122) permits eating microscopically viewed bugs if they cannot be seen by the naked eye.
R' CO Grodzenski is quoted (source needed) as permitting microscopic bugs.
R' SZ Aurbach (quoted in SSK 3:37) permitted eating microscopic bugs.
R' YS Elyashiv permits microscopic bugs if they will always remain microscopic.
I haven't read the above from their original sources.