In either case, removing with something other than the program that created those data stores will corrupt them. You should note that there are some cases where threat files really shouldn't be removed by anti-malware software, such as when those files are in Time Machine backups or Mail mailboxes. Note that if you're seeing discrepancies between Kaspersky and Malwarebytes for Mac, there are many potential explanations: There is Malwarebytes software for Mac business users, but it uses the same engine as the consumer product.