If you have applied for a passport on or before 2009, you would probably remember going to the old Department of Foreign Affairs (DFA) Main Office along Roxas Boulevard near the Asian Institute of Maritime Studies. But now, they have a new office near the S & R Building a few blocks from the SM Mall of Asia. (Refer to the image below).
Image from Google Maps
To get to the new DFA office, you can take a bus going to Baclaran and tell the driver to drop you off the new DFA office near the S & R building. The S & R building will be very visible along Roxas Boulevard due to its huge logo. From Roxas Boulevard, you would have to walk for several minutes until you get to the S & R building and just behind that is the DFA's new office.
Another way of getting to the new DFA office is to go down the Taft MRT station and ask for directions where to ride small vans modified to resemble Philippine Jeepneys. Their logo will state "DFA Bago". Fare is about 10 pesos. This is the same convenient method of getting back to the MRT station from the DFA since these mini vans pass directly in front of the DFA building. Be careful not to ride Philippine Jeepneys that say DFA in their logo since these will take you to the old / original DFA building.
Once at the DFA office, tell the guards that you are applying for Passport Certification or Certified True Copy (CTC) of your passport. You should already have a photocopy of your passport's front page (the one with your picture) and back page (the one with your signature), and a photocopy of a valid I.D. These requirements are stated on the application form you will fill out during the interview process. Proceed to Door number 5 and again, state that you are applying for Passport Certification or Certified True Copy (CTC) of your passport.
At the Interview Area, make sure you inform the guards of your application so that they can provide you with a queue slip, which you will fill out with your name, and the reason you are there. You might have to wait for about an hour depending on the number of people ahead of you. During the interview, you will be asked why you are applying for Passport Certification of CTC, and how many copies you will need. Once approved, you will have to pay 100 pesos per copy. You will be given a receipt which you will have to pay at the cashier's office, at the 2nd Floor.
Once you've paid, return the duplicate copy to your interviewer and ask for the date you can claim the Passport Certification. It will usually take 5 business days.
I tried applying for Passport Certification from DFA Mega Mall, but they said they no longer entertain these requests since their turn around time for one was 15 business days. They now encourage applicants to proceed directly to the new DFA office.
I hope you find this information helpful. And as for the DFA, I hope you can improve your queuing systems similar to that of Quezon City Hall where you are given a number and a screen will denote your position in the queue. This suggestion will hopefully result in a faster and orderly queue.