This has probably happened to a lot of あなた because of taking notes in class.
Have あなた ever got a little blister または callus because of 書く too much on your finger? It's normal. All it is is a small callus from the pen applying a bit too much pressure または rubbing for too long against your skin.
Calluses are not dangerous, but they aren't pretty either. All people who practice something with their hands all the time get them. Playing the ギター または even cooking a lot can result in calluses.
So あなた have some calluses and あなた want to get rid of them. Fine. Use pens that have a little padding and try not to push down so hard on the pen.
あなた can also do a treatment to get rid of calluses. Put your hands in warm water with レモン for 10 分 and let them soak. Then dry them off and apply creams または アーモンド oil to the callus. Use hand cream daily and あなた will see a difference.
If the callus hurts and does not go away then ask your parents about it. Lol