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eTMF systems usually have guided steps for a user to complete a particular process such as certifying a record as a copy. The first minute of this video shows what that process looks like to an end user in one particular site eTMF system (I am not trying to be self-promotional, but linking to this video is much more effective answer than trying to describe it in words here).
An organization’s SOPs should provide guidance as to when their staff would need to execute such a process (some organizations may not actually destroy certain paper records, thus even if uploaded to a system those records would not need to be certified as copies).
If an organization does not have an eTMF system or if for some reason a certified PAPER copy of an original paper record needed to be generated, I don’t know of a ‘typical’ approach…but off the top of my head, I could see something like a ‘certified copy attestment’ page being appended to the copy and signed by the person who declared the copy a true reproduction of the original.