We want to make sure that the file is a valid format of the file that it says that it is. Examples: Is the file MyFile.PDF a valid PDF file? Is the file MyFile.xlsx a valid Excel file?
I don't think such a global tool or methodology exists, probably for a good reason.
Taking even PDF or XLSX, how do you even establish if the format is valid? If Acrobat or Excel can be automated programmatically to open them, they're presumably almost certainly valid, so you could check that for each file type. That's probably the most you could hope to achieve. Maybe check the file header for the byte signature of the file types, but does a database of those signatures exist for every type you might have to deal with?
Going further would you really want to re-engineer all the code those applications have to open a file and populate the required internal memory structures and figure out what internal checks they do to decide "yep, that looks OK" ?