It might be a long shot, but is it possible that the word is
I am used to modify a sentence.
In law, a rule is defined as an order made by a judge to modify a sentence
I can be used between two letters, and I can be used to swap two letters.
These are similar in that they could refer to math. You can use a rule between two letters (ie variables):
a > b. In a similar way, you can use a rule to swap two letters:
a = b. While I naturally considered math/programming rather than regular English, seeing that you're a mathematician from your profile further influenced my decision to stick to this meaning.
My prefix is commonly used
A bit of a long shot but the most common use for the prefix (RUL) is within the medical field, meaning Right Upper Lobe [of a lung]. Our lungs are pretty commonly used, I'd say.
my suffix is sometimes found in remote places.
Again, unlikely, but a Ule is a type of tree that can be found in rainforests of Mexico, Central America, and northern South America. A rainforest is more often than not considered remote, as it is far from civilization and difficult to get to.