Thanks AMA. I changed the plotting order and again weird result. First image is bigger than the second and third.

Thanks a lot @Michael for detailed explanation!

Thanks a lot JRR for detailed explanation, and sorry for confusion with e1071.

Thanks JRR, I added R code for calculating skewness and kurtosis.

Thanks @Roo, I don't think this helps. Because I don't have a criteria to select/separate those noise points.

Thank you @MichaelStimson. I am thinking of purchasing lastools and I found Martin has a wonderful tutorial for solving similar problem rapidlasso.com/2018/04/09/…. Unfortunately, I don't have ground control points to use for matching flight lines.