If you need to clip according to a bounding box ... you can define it using coordinate filters (in X, Y and/or Z) using for example, las2las.
If you need to clip according to an irregular shape (defined by txt file or SHP file) ... in my knowledge, you only extract your data that is included in this/these polygon(s).
It is important to consider that LAStools is designed basically for aerial LiDAR data treatment (although it may have applications to data cloud processing in other contexts, e.g., ground captures, etc.). You can define a bounding box and then apply the lasclip for the irregular shape. Also you can rotate your data using las2las, but logically always, data and clipping polygon must be in the same reference system.
If possible, it would be advisable to provide an example of what you want to do, so that it can be easier to guide you..
Jorge