An approach to determine cantilever movement is presented. An observer based state estimation and statistical signal detection and estimation techniques are applied to Atomic Force Microscopes. A first mode approximation model of the cantilever is considered and a Kalman filter is designed to estimate the dynamic states. The tip-sample interaction is modeled as an impulsive force applied to the cantilever in order to detect the presence of sample. A generalized likelihood ratio test is performed to obtain the decision rule and the maximum likelihood estimation of the unknown arrival time of the sample profile and unknown magnitude of it. The use of the transient data results in sample detection at least ten times faster than using the steady state characteristics.