The interactions between argon surface nanobubbles and AFM tips on HOPG (highly oriented pyrolitic graphite) in water and the concomitant nanobubble deformation were analyzed as a function of position on the nanobubbles in a combined tapping mode and force volume mode AFM study with hydrophilic and hydrophobic AFM tips. On the basis of the detailed analysis of force distance curves acquired on the bubbles, we found that for hydrophobic tips the bubble interface may jump toward the tip and that the tip bubble interaction strength and the magnitude of the bubble deformation were functions of vertical and horizontal position of the tip on the bubble and depended on the bubble size and tip size and functionality. The spatial variation is attributed to long-range attractive forces originating from the substrate under the bubbles, which dominate the interaction at the bubble rim. The nonuniform bubble deformation leads to a nonuniform underestimation of the bubble height, width, and contact angle in conventional AFM height data. In particular, scanning with a hydrophobic tip resulted in severe bubble deformation and distorted information in the AFM height image. For a typical nanobubble, the upward deformation may extend up to tens of nanometers above the unperturbed bubble height, and the lateral deformation may constitute 20% of the bubble width. Therefore, only scanning with a hydrophilic tip and no direct contact between the tip and the bubble may reduce nanobubble deformation and provide reliable AFM images that can be used to estimate adequately the unperturbed nanobubble dimensions. The deformation of the bubble shape and underestimation of the bubble size lead to the conclusion that the profile of surface nanobubbles is much closer than previously thought to a nearly flat bubble profile and hence that the Laplace pressure is much closer to the atmospheric pressure. Together with line pinning, this may explain the long nanobubble lifetimes observed previously. The findings presented in this report hold independently of the material that constitutes the interrogated nanoscale surface features.