Yes! As clean as possible. If you are diluting in water, use the cleanest water you can find. Remember, AFM is a SURFACE microscopy technique and it shows EVERYTHING at the surface. If your 3mm thick sample has only a 3nm contamination layer, you might see NONE of the sample!

Here are a few results on water quality. It’s not based on a statistically significant number of samples, and is based on MY water supply, so your mileage may vary, but it should give you an idea of the RELATIVE qualities of various water sources. The way I did it was depositing a drop of water and drying it on freshly cleaved mica. Then the sample was scanned with AFM. The Ra value for mica was about 0.05 nm.