You could retrieve all FileDocuments where the owner is the CurrentUser using an XPath query. You can then delete these matching FileDocuments.
You have to Create a XPath Query for resepected User and retrive Uploaded file from Database and then you can delete data with respect to users.
You can follow the following documentation for your doubt.
When you create a document entity it will be generalized from System.FileDocument. All of the system members (createdDate, changedData, owner and changedBy) are automatically stored once a new object is created of your document.
To find the documents that are created by the current users you can use the following Xpath:
[System.owner = $currentUser]
This will give the list that the currentuser has created. Then you can delete that list in your microflows.