position of "only"

(A) Mosquito larvae can only be seen through a microscope.
(B) Mosquito larvae can be only seen through a microscope.
(C) Mosquito larvae can be seen only through a microscope.

As pointed out in this answer, only focusses on another constituent in the sentence, which is usually stressed, and which controls where only can appear in the sentence.
The rule is that only may appear
either

• Immediately before its focus,

or

• Immediately before any constituent that contains its focus.
  (exactly like Russian dolls)

(B) is a little unusual, but not incorrect. (A) and (C) are both fine. They all mean the same thing, but each has different possibilities for focus, viz:

• (C) means that either a microscope or through a microscope is the focus of only.
• (B) means either the verb seen or the verb phrase seen through a microscope
  (a focus on seen is unusual, unless it is contrastively stressed to mean (e.g) 'not heard')
• (A) means that any of the above constituents can be focus.

Some people might not like (B) because the normal place for operators like negatives and only is after the first auxiliary verb, and (B) places only after the second one. However, auxiliaries are elided and contracted so often in English that the difference isn't really important or even perceptible, especially since only is much more complex than a simple negative like not.

I'm willing, I guess, to be the foil to John Lawler and his sagacious answer and add a few not-so-sage sentences.

With the advanced photographic technology available to us today, we can see mosquito larvae quite nicely, thank you, in pictures. Hence, option (C) requires slight modification. E.g.,

"Mosquito larvae can be seen only through a microscope or in a picture taken by a PAXcam digital camera via fluorescence microscopy used in cell biology studies."

Or, much more simply:

Mosquito larvae can be seen only through a microscope or in a picture taken by a PAXcam digital camera."

As for options (A) and (B), each is likely to be heard today coming from folks who lack a certain, uh, preciseness in their speaking and writing. Let me be quick to point out, however, imprecision does not necessarily equate with incorrectness. If you understand what a person is saying, who cares if s/he says it in a less-than-precise way. More often than not, drawing attention to a misplaced only will leave you only feeling embarrassed (or is that "leave you feeling only embarrassed"? or "only leave you feeling embarrassed"?).