Well you will have to go to the excise office of Islamabad. It is located in F-8 Markaz.
You will have to take all the documents of this ride including:
1) Aution sheet
2) Export certificate
3) Port landing documents (Bill of landing, Bill of entry)
4) Other Invoices like tax recipets
5) Copy of passport of the person who imported the car
6) A proof that you live in Islamabad. E.g. your utility bill
7) A copy of NIC.
You will write an application to the Excise & Taxation Officer for new vehicle registration. The forms are available online at Excise and Taxation Department website.
The process is simple but feels bad as a lot of time is involved. There are multiple windows. Each numbered (1,2,3,4,5) and the purpose of window is also mentioned on top of it. You will go on each window step by step.
a) You will present documents
b) You will be provided with a challan form. You will fill it with the money required. Fee is normally a combination of Registration fee, Token tax, any late processing fee (as a car should be registered before two months of it's arrival at Karachi port else you will fill a fine) etc.
c) You will go to the bank and submit the money.(National Bank F-8 Markaz is closest but has long queues at cashier booths :().
d) You will come back from bank and collect the "F" from.
e) After that you will have to take your ride to inspector who will inspect the vehicle for engine and body number. He will write the information on the F form and final verification signature would be done. (Now a days they inspect vehicles in Fatima Jinnah park).
f) In the end you will submit all the papers.
G) You will get the registration reciept same day. But you will get the number plates in a week. You will get original copy through mail in one to six months.
Frankly speaking I hate this process. Simply go to agent. Give him money and all documents. Simply take the receipt and number plates from him after registration. Normally they take 2000Rs for the process.