There is an array containing 3D data of shape e.g. (64,64,64), how do you plot a plane given by a point and a normal (similar to hkl planes in crystallography), through this
This is funny, a similar question I replied to just today. The way to go is: interpolation. You can use griddata from scipy.interpolate:
Griddata
This page features a very nice example, and the signature of the function is really close to your data.
You still have to somehow define the points on you plane for which you want to interpolate the data. I will have a look at this, my linear algebra lessons where a couple of years ago