We use a PDMS transfer technique, where we exfoliate the black phosphorus on the PDMS first and then dry transfer it to SiO2/Si substrate.
Are you sure that the AFM is calibrated? The best way to measure the nano scale samples are SEM and Focused Ion Beam (FIB).
2 nm is around 10 atomic layers of phosphorus. I'm suspicious of anything that small in terms of reproducing it over any reasoanble area.
Also keep in mind that the quantification of height by AFM at these scales is affected tip-sample interactions. Typically, you make a cross-section between your 2D layer and the substrate. If the substrate is SiO2/Si then you already have a difference in the tip-sample interaction between the SiO2 and the 2D material. This difference in sample interaction due hydrophobicity, electrostatics, or van der Waals could mess up the quantification of the height difference you obtain.
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