If it says to take a certain antibiotic 3 times a day, does that mean i can take it at 9am, 3pm and 9pm? or do i have to take it in middle of night?

9/3/9 ok: Three times a day is ok as you have it. "every 8 hours" might require you to get up at night.

Antibiotic Dosage: Generally, if the rx is written for three times a day, you can take the 3 doses, spaced equally, during waking hours. It is best to call your pharmacist to be absolutely sure, however, because you want to make sure you maintain minimum levels between dosing. In your case, you have 2 six hour cycles, followed by a 12-hour "gap." as long as the concentration is adequate during the night, it's ok.