Multipath effects on carrier phase measurements are the major error source for short baseline positioning. Multipath effects impair the precision and reliability of both the ambiguity resolution and estimated site coordinates. Empirical Mode Decomposition (EMD) is a relatively new non-linear technique for adaptively representing non-stationary signals. The method is a fully data driven approach. Noisy signal is decomposed adaptively into oscillatory components called Intrinsic Mode Functions (IMF). A data filtering method, based on the EMD, is employed for separating signals from noise in data series, and applied to mitigate carrier phase multipath effects. The EMD based multipath mitigation scheme is suggested and experimental results show that the method can be used to successfully mitigate multipath, the results also show that the ambiguity solutions become more reliable after multipath correction.