I'm way late on this I know, but just saw the post.
Here in Peru US$100 bills are very common and normally are no problem to use if you are paying for a high priced item. Yes, they will look at them very carefully, as they do with any bills, US or Peruvian. They know the difference between real and fake. As was said they must be almost like new - any rips or tears and they will refuse them. You MIGHT be able to exchange them for soles at a money changer but they will not give you the full rate for them.
If you have a large amount to exchange, they prefer $100's. There was a group here trying to exchange about $5000 in US $20 bills and the money changer refused them, said it was too many bills.
Also don't try buying any low priced item with a large bill, most places don't have much change on hand. An exception is the large supermarkets and drug stores, where you can pay in soles or dollars, they have a lot more cash on hand. Out in the villages you need to have almost exact change.
A money belt is a good idea, don't keep much money (or cards - credit or debit) in you wallet, the pickpockets are very good here.