Don't delete the data. Data storage is cheap these days so just keep it. If you're talking about removing the data from your mat files, that's another story.
Option 1 is to only import the data you need in the first place. It's much more efficient to import only the needed data rather than importing all of the data and then removing what's not needed.
Option 2, if you've already got your mat files and you have the need to clean them up or reduce file size, assuming the data you want to remove is stored somewhere else for future reference, here's how to remove selected variables:
Assuming your mat file is loaded into the workspace, remove variables "var1" and "var2" like this:
clear('var1', 'var2');
Then save your mat file, overwriting the existing file.
If you're trying to remove variables from a mat file that isn't loaded into the workspace, see this (I've never used). https://www.mathworks.com/matlabcentral/answers/254048-how-can-i-delete-variables-in-my-mat-file-without-loading-them-into-matlab-7-2-r2006a#comment_472754
