If you're asking how to apply the rotation matrix R to rotate a point P=[x;y;z], you would just use matrix multiplication Pnew=R*P.
Note, however, that ABSOR calculates a translation vector, t, as well (and sometimes also a scaling if you select the doScale option). The full transformation would be Pnew=R*P+t.
Finally, if you are working in homogeneous coordinates P=[x;y;z;1], ABSOR also returns a 4x4 total transformation matrix M. In that case, the transformation can then be done Pnew=M*P.
Thank you to provide this very useful toolbox. I have a question: if I obtain the rotation matrix from your method, then how can I get the coordinates of any point in the new coordinate system (target).