The Is/Is Not tool can be used for both the problem definition and as a root cause analysis tool. For the latter, you can take one of many routes.
One option is to directly use the Is/Is Not table from the problem definition, list out the causes that could have led to the “Is” versus the “Is Not”, and evaluate how many of the “Is” and “Is Not” problem definition items might be explained by each of the causes (more Is/Is Not problem definition items explained = more likely to be a root cause).
Another option is to have the problem defined first, then use a matrix of what, where, when, and magnitude questions to organize information about the problem. For each Is/Is Not difference, consider the potential causes.