How did you create these multiple figures? If in a loop and retrieving names based on some other info, then when find the next of the same name, plot it into its associated axes handle at the time...then you don't have to merge anything later.
If you're using same code repeated with different variable names, then learn to use cell arrays or variable field names with struct or other ways to avoid storing metadata into variable names.
Let's see how you're going about it and solve the underlying problem instead of having to clean up afterwards...
