What do I do if husband was incarcerated, got out and came to live in my apartment but I don't want him here?

Evict him.

If it is your apartment, you can give notice to terminate the tenancy of your husband and then commence evictions proceedings. You could also give notice of the change in terms of the tenancy and charge a high rent. This answer assumes that this is indeed your apartment and that you are on the lease or rental agreement and that you obtained the apartment after you and your husband separated. In a divorce proceeding you can also ask a judge to grant you possession and control of the apartment.

I am sorry you have to deal with this situation. Because you are married you cannot evict a person from their own home/apartment. Of course you could move out. If that is not an option, then you need to file for a divorce as soon as possible. Your attorney can file the appropriate motions to deal with residency. Although he was incarcerated, please understand that you are still married and tied together legally.

I suggest you call the police, if he is truly an intruder. If not, you will need to go through a legal eviction process to get him out.