Heavy ion beam probe (HIBP) is an excellent diagnostic to measure the density and potential fluctuations simultaneously in magnetically confined plasmas. However, it has been well known that the density fluctuation measured with the HIBP is not local but contains the fluctuations along the beam orbits. In this article, a method is proposed to evaluate local density fluctuation in the HIBP measurements by removing the well-known path integral effects. The reconstructed density fluctuation amplitude and power spectrum are shown, for example, by applying the proposed method on the density fluctuation measurement data obtained in a toroidal helical plasma, Compact Helical System.