Sorry, but I have to disagree with Bert on this subject. For five years I lived in Bali with a SB...social cutural visa. I was finger-printed twice, and oddly, it was each finger of each hand...what a mess of black ink! This fingerprinting was required by immigration, not the police.
Yes, upon arrival at your intended long stay location, and with any visa other than a tourist visa, reporting to the nearest police station is expected, and required. By this, you are in effect, only "checking in" and in fact, it's a good idea.
No, if you are not going to be staying in Semarang, there is no need to report yourself to local police station there, or in Jakarta either, if as you say, you are headed to Irian Jaya. You mentioned Papua, but I'm assuming you ment Irian Jaya, Indonesia.
Once in Irian Jaya however, you should most certainly report your presence, and visa status to the local police. They may, or may not require fingerprints.
If you wish to travel in the more remote areas of Indonesia, certain requirements are expected above and beyond the more frequented travel destinations. These requirements are intended for your own safety, and, in the event of bad luck, identification of your remains...if there are any.
Just kidding...well, sort of anyway.