Number of layers = Total thickness obtained from AFM / single layer of graphene oxide or reduced graphene oxide.
Theoretically, single layer graphene thickness is 3.35Å reported for layer-to-layer carbon atom distance of graphite crystals. Practically 1-1.5 nm would be considered for single layer GO or rGO, depending on the modes of operation.
I think AFM is better to measure the number of layers. Alternatively, you can use Raman spectroscopy. Depending on the position and shape of 2D band, you can understand the layers
Find the inter spacing distance by using Brag law you get the inter spacaing distance, then divid the thickness by interspacing, then you will get approximate number of layers.
First, calculate the crystallite size of sample then divide by interlayer spacing then it will give you roughly(~3 layer error) idea about your number of layers .