EISCAT VHF radar data are used for observing, monitoring, and understanding Earth’s upper atmosphere. This paper presents an approach to segment Polar Mesospheric Summer Echoes (PMSE) from datasets obtained from EISCAT VHF radar data. The data consist of 30 observations days, corresponding to 56,250 data samples. We manually labeled the data into three different categories: PMSE, Ionospheric background, and Background noise. For segmentation, we employed random forests on a set of simple features. These features include: altitude derivative, time derivative, mean, median, standard deviation, minimum, and maximum values corresponding to neighborhood sizes ranging from 3 by 3 to 11 by 11 pixels. Next, in order to reduce the model bias and variance, we employed a method that decreases the weight applied to pixel labels with large uncertainty. Our results indicate that, first, it is possible to segment PMSE from the data using random forests. Second, the weighted-down labels technique improves the performance of the random forests method.