LiDAR is an excellent source of elevation data used in many surveys. The spaceborne handle system, Global Ecosystem Dynamics Investigation (GEDI), provides ground elevation information with high accuracy except for areas with steep slopes. GEDI data have a lot of noise from atmospheric conditions, and therefore filtering procedures are mandatory to select the best dataset. The dataset presents uncertainties of different magnitudes, with values reaching more than 100 m of difference between the reference data and the GEDI data. The challenge is to find a criterion to determine a threshold to filter accurate GEDI samples. This research aims to identify the threshold based on the difference values between the reference data and the GEDI data to select the maximum number of samples with low RMSE values. Therefore, we used the Kolmogorov–Smirnov (KS) non-parametric test to define the best threshold based on a normal distribution. Our results demonstrated a lower RMSE value with a high number of samples when compared with the quality flag parameter threshold, even using sensitivity parameter thresholds. This method is useful for achieving the best possible accuracy from GEDI data worldwide.