I presume you mean the 3D Cartesian Coordinate Rotation VIs. The NI documentation has a decent description of what they do: https://zone.ni.com/reference/en-XX/help/371361R-01/gmath/3d_cartesian_coordinate_rotation_euler/
These are polymorphic VIs. By default, they take an array of coordinates. If you just want to rotate a single point, select the "Scalar" version of the VI (Put the subVI on your block diagram, then Right-click > Visible Items > Polymorphic VI Selector)
The 3x3 matrix is the transformation matrix, which is a concept described in linear algebra. There are different types of transformations: Translation, rotation, shearing, scaling, etc.
In a nutshell: Think of your 3D point-coordinates as a 3x1 matrix (also called a column vector). If you multiply a column vector by a 3x3 matrix, you will get a new column vector. That new vector will contain your "transformed" point-coordinates.