Read data in Matlab for MIKE 3 with hybrid vertical grid

Hi,

I am using MIKE 3 for my simulation work, where I have used MIKE 3 in open ocean. I have configured my model with a hybrid sigma and z vertical grid.

I am now trying to understand how to process the data. I have looked at the example given in the Matlab toolbox. I am a bit confused on how to proceed. I understand the workflow on how to use the data in Matlab, but there is an inherent assumption that the data can be reshaped for number of elements in the
model grid and the number of layers, however when I try to do that i do not get the same number of elements as i have put in the model grid domain.

My initial thought is that when the grid is created in the output of MIKE 3, it does not provide any information of the places where z coordinates makes the stepped mountain when it encounters land with depth. I was wondering if any one has some suggestion on how to deal with it. Also, I would like to know how to provide the vertical grid setup (more like best practice). Right now I am doing more of a hit and trial.