First of all, it's RMSE, not RSME. It stands for Root Mean Square Error:
https://en.wikipedia.org/wiki/Root-mean-square_deviation
With 3D coordinates you can compare component wise, or however else you choose to define a distance measure. Then you plug this into the RMSE formula. Essentially this means comparing an expected value to your observed value.
As for the point correspondence - this depends on the algorithm of choice. Probably one of the most famous examples is ICP:
https://de.wikipedia.org/wiki/Iterative_Closest_Point_Algorithm
In a nutshell for every point of one cloud, the closest point of the other cloud is determined. Then an error measure is calculated and lastly points are transformed. This is done an arbitrary number of times, depending on the desired precision.
Since I strongly suspect that you are indeed looking for ICP, here is the description as to how they are put together:
https://en.wikipedia.org/wiki/Iterative_closest_point
Other than that you will have to do some reading yourself.