Hi David,
thanks for the positive feedback about las3dpoly :)
The tool should be able to cut or classify along polylines and polygons.
A simple test out of our demo data:
las3dpoly64 -i lake.laz -poly lake_breakline.shp -o tmp.laz -distance 4 -remove_points
lake_breakline.shp is a polygon:
The result shows the lake line without borders:
If this don't work with your data: Please provide a small sample and we will have a look.
Cheers,
Jochen @rapidlasso