The below would be easier if you only had one variable stored in the .mat file and you knew the name of the variable. The below code does not assume that there is only one variable and does not assume that the variables have any particular names; the code takes the first three columns of all of the variables that are present, and creates the new .mat file using all of the same variable names.
filename = 'YourFile.mat';
newfile = 'YourNewFile.mat';
datastruct = load(filename);
newstruct = structfun(@(M) M(:,1:3), datastruct, 'uniform', 0);
save(newfile, 'newstruct', '-struct');
