Thanks for getting in touch. The VariableSet's Variables is an IList, so it has an Add and a Remove method. The Remove requires an object though, so you'd have to look through the list for the variable that has the name and ScopeSpecification that you're after and then pass that object instance to the Remove method.
For completeness, there is also a RemoveAt but I suspect a remove based on index position won't be what you're after.
Hope that helps and if I can assist further just let me know.