Serial port time out question

I am using the serial port to actively check to see if a RFID tag is present. If it is then i want to read the data and continue what i was doing, all the while checking to see if there is more data to be looked at. I have set my read timeout to 1000 (a sec). If i call the procedure that executes the serial port read and there is no tag it should time out (correct ). If there is a tag it will read it. I want to check the serial port every second. Is this possible I also in debugging have noticed that when it recieves a timeout that it gives me a "time out notification" is this only in debugging or when i am using the final project will this go away

Thanks

colt