I agree with Erie H Morales - check the discussion performed some time ago. Briefly you can measure the thickness by profilometry (you will need high sensitive equipment for thinner film), by ellipsometry or using transmittance and/or reflectance spectra and non linear curve fitting. If your film is thick enough (let say more than 500 nm), transparent and deposited on non-absorbing substrate with known optical constants you can use Swanepoel's method. Hopefully this help.
A highly sensitive AFM may give you a good thickness profile. SEM (Field emission is better). Elliposometry and reflectance measurements would give you indirect measurements, but the problem is that you really need a direct thickness profile if you do not expect your film to be even.