The interaction between a vortex within a finite-thickness type-II superconductor and a magnetic force microscopy tip is studied. By analyzing the expression of the arising lateral force, we show that the superconducting penetration depth may be recovered from experiment, using the so-called Laplace transform inversion method. This entails a vertical displacement experiment. The consideration of lateral scanning modes has allowed us to extend the theory to the more stable Hankel transform inversion method, which eventually becomes a Fourier analysis application. For the case of vortices in two-layered superconductors, we show that magnetic particle manipulation is possible by tuning the configuration of the layers.