Suppose I run a script X.m and it creates a bunch of variables, and I want to save a variable called Z, so I write myVar = Z.
You can use clearvars to clear all variables except specific ones from workspace. From clearvars documentation:
clearvars -except v1 v2 ... clears all variables except for those specified following the -except flag. Use the wildcard character '' in a variable name to exclude variables that match a pattern from being cleared. clearvars -except X clears all the variables in the current workspace, except for those that start with X, for instance. Use clearvars -except to keep the variables you want and remove all others.
So, you need to type
clearvars -except myVars
instead of clear.
There's Keep on the MATLAB file exchange which lets you clear everything except certain variables that you wish to keep.