Usually it is enough that the player said he is "searching the room". It is assumed that the PC is going around the room searching through boxes, examining walls, etc. It is supposed to take minutes to complete and can be considered to test for anything requiring a perception check. Rarely is perception meant to target a specific square.
Now, if there's a chest that has a specific hidden compartment inside it (a false bottom, perhaps), you may want to require a specific perception from whomever opens that chest.
Elves used to get a free perception check to notice secret doors if they were wihtin 5' of them, this was taken out.
Dwarves DO get a free perception check to notice secret doors if htey are within 10 feet of htem sand it invovles stonework.
So unless the person is searching an area, or a dwarf and the door invivles stonework, (it takes a move action to search a 5' x 5' square) he would not notice the secret door even if he rolled a 100 on his quick perception check from the doorway. He is getting a general feel for the room rather then searching specific things.*
*Some people will disagree and say that the one perception should allow it with a -1 for every 10' away. I disagree, I would allow them to seach a square for secret doors from 40' away at a -4, but they would have to declare they are spending that move action searching that square.
So if a person stood in the middle of a 20 x 20 room and spun around in a circle slowly looking for secret doors I would let him make a perception check at -1 (10 feet from a wall)and it would take him 16 move actions to check the 80 feet of wall. I would not let him walk into the room make a percepption check as a move action and note three secret doors even if he had a +100 perception.
In practice, our group typically requires a Perception check after a player declares they are searching for a secret door in the room. We don't require them to specify a location (old school D&D used to require targeting a specific 10x10 square). Usually everyone in the party is checking, so someone is bound to make the check and find the door. I have no idea if this is the "official" way to do it, but it's quick and clean and works for us.
Also, our group also requires more specificity when searching for traps. What exactly is the character searching for traps? A chest, a lock, a doorway? In this case, the specific details could be important.