Rotating and working on MATLAB 3D objects - matlab

Question

How do you rotate 3D objects around each of the three axes when coordinates are of MATLAB style (X, Y and Z kept in different arrays).
This code is a start. I think I have found the rotation matrix (for pi/2 rotation around x), here it is called rotX90_2. But how should rotX90_2 operate on X, Y, Z?
[X,Y,Z] = cylinder;
% rotX90_1 = makehgtform('xrotate',pi/2) gives
rotX90_1 = ...
[1 0 0 0;
0 0 -1 0;
0 1 0 0;
0 0 0 1];
rotX90_2 = rotX90_1(1:3, 1:3);
% Here rotX90_2 should operate on [X,Y,Z] in order to ...
% rotate it 90 degrees around x, but how is this done?
% == What code should be put here to rotate the cylinder? ==
surf(X,Y,Z);
I have just started using MATLAB. As I understand, the basic ways to manipulate 3D graphics are to either operate on the X, Y, Z, like here or, you can first run graphics routines like h = surf(X, Y, Z); and then operate on graphics objects, using f.ex. hgtransform.
It is convenient to translate and scale using X, Y, Z. - You just add and multiply by scalars. But I ask this question to understand how to rotate.
If you operate on the graphic objects, on the other hand, you can use the function hgtransform. But you must then first create other objects, since hgtransform does not operate directly on the graphic objects, as I understand. (Except functions like rotatex(h, angle). F.ex, I have not found a corresponding "translatex(h, distance)". That surprised me. Maybe I didn't look well enough.)
OK I am new to this. Any simple, practical pointers how to easily rotate, scale and translate MATLAB 3D coordinates/objects (around the coordinate system axes) would be appreciated.
Edit:
According to Prakhar's answer below, which works, the code needed to fill the gap above is the following. Thank you, Prakhar.
[row, col] = size(X);
coordinates = [reshape(X, [row*col, 1]), reshape(Y, [row*col, 1]), reshape(Z, [row*col, 1])];
rC = coordinates * rotX90_2;
X = reshape(rC(:, 1), [row, col]);
Y = reshape(rC(:, 2), [row, col]);
Z = reshape(rC(:, 3), [row, col]);

Answer 1

Let's say R is the appropriate 3x3 rotation matrix.
coordinates = [X Y Z];
rotatedCoordinates = coordinates * R;
(Assuming X, Y, and Z are column vectors of same size)
Now, you can get the new X, Y, and Z coordinates from rotatedCoordinates as rotatedCoordinates(:, 1), rotatedCoordinates(:, 2), and rotatedCoordinates(:, 3), respectively.
EDIT: Another alternative when X, Y, Z are 2D matrices:
[X, Y, Z] = cylinder;
[row, col] = size(X);
coordinates = [reshape(X, [row*col, 1]), reshape(Y, [row*col, 1]), reshape(Z, [row*col, 1])];
rC = coordinates*R;
Xn = reshape(rC(:, 1), [row, col]);
Yn = reshape(rC(:, 2), [row, col]);
Zn = reshape(rC(:, 3), [row, col]);