Specifically, I am trying to say something like "a semester's length is counted in months" in order to imply how short it is as compared to, say, your whole life. When I tried to look this up in my online dictionary, I could not find anything. There was an entry for "count in" but it was definitely a separate meaning ("count me in!")
There is also 何ヶ月, as in
which I think fits even better for your purpose. 数ヶ月 is more a specific length in time, although you choose not to specify the length. 何ヶ月 means that you are counting in months, but have no real estimate of how many months.
何 works for "counting in" with other counters, e.g.
I waited for hours.
I waited for several hours.
I love (Japanese) prawn crackers. I couldn't stop eating.
Getting my visa wasn't a matter of days, but a matter of weeks.
Edit: Since you seemed to be asking something different, the way for translating "is counted in" is で数える, as in
You can count fish with the counter word 尾.
If it just means “One semester is a few months long,” it can be 学期の長さは数か月だ. “A few months” in English is probably two or three months, but 数か月 in Japanese can be somewhat longer. See question “Why use 数年 in あれから１０数年?” for more about this usage of 数.
A related expression, 月単位の時間, has a similar meaning, but it refers to the abstract notion of time directly. For example:
この作品の完成には月単位の時間がかかる。 It takes months to finish this work.
However, in your case, 学期の長さは月単位の時間だ is probably not incorrect, but it sounds awkward, probably because 長さ and 時間 refer to the same thing.