First locate the main police station in your area. Try calling them up and asking them where to get a police clearance. Go to the one neareast to you. Usually, it is only in the main branch that one can get a police clearance.
Go to the city treasurer's office and pay for your documentary stamps which usually costs 40 pesos. Just tell the teller that you're going to pay for the police clearance. Usually, the city treasurer's office is inside the city hall.
After paying, you'll be given a receipt. Present this receipt at the police station. And then you'll be given a form to fill up. After filling it up give it (and the receipt) to the officer and pay them 60 pesos.
Your name would then be called up. When you hear your name, your picture will be taken. After that your name will be called again. This time your police clearance will already be given to you. Then ask the guard or officer to take your thumb mark.
That's it! You're done!
Remember that the process is not the same in all police stations in the Philippines. However, I am sure that any difference will not be that significant. I actually got my police clearance from the Zamboanga city police station main branch.
Just a disclaimer: I am not connected to any government office so I won't be able to answer any questions that you might have regarding procedures and processes on how to procure documents such as an NBI clearance, an NSO authenticated birth certificate, and etc. All the information that I have is already presented above. The information presented in this post was gathered when I transacted with the Zamboanga city (region 9) branch/office.