Merge multiple Point Clouds into a single 3D object
CloudCompare has statistical outlier removal (called SOR) function that can eliminate all lonely points for you. I would filter each *.ply first and then try to carry out a cloud to cloud registration. For registration, you can use MeshLab or use 30 days trails of commercially available software such as Faro Scene. Scene won't accept *.ply file though, so you need to convert your files to *.e57 first. Good luck.