Airborne LiDAR produced large amounts of data for archaeological research over the past decade. Labeling this type of archaeological data is a tedious process. We used a data set from Pacunam LiDAR Initiative survey of lowland Maya region in Guatemala. The data set contains ancient Maya structures that were manually labeled, and ground verified to a large extent. We have built and compared two deep learning-based models, U-Net and Mask R-CNN, for semantic segmentation. The segmentation models were used in two tasks: identification of areas of ancient construction activity, and identification of the remnants of ancient Maya buildings. The U-Net based model performed better in both tasks and was capable of correctly identifying 60–66% of all objects, and 74–81% of medium sized objects. The quality of the resulting prediction was evaluated using a variety of quantifiers. Furthermore, we discuss the problems of re-purposing the archaeological style labeling for production of valid machine learning training sets. Ultimately, we outline the value of these models for archaeological research and present the road map to produce a useful decision support system for recognition of ancient objects in LiDAR data.