WhiteboxToolsWhiteboxTools can clip a LAS file to multiple polygons contained within a Shapefile using the ClipLidarToPolygonClipLidarToPolygon
tool. Using Python scripting, you can use the tool as follows:
from WBT.whitebox_tools import WhiteboxTools
wbt = WhiteboxTools()
wbt.work_dir = "/path/to/data/"
wbt.clip_lidar_to_polygon(i="input.las", polygons="polygons.shp", ouput="ouput.las")
Or, if you prefer a GUI, you may use the QGIS based plugin or the WhiteboxTools Runner, which is distributed (wb_runner.py) with the binary download of the library: