Is it a small set of customers, or hundreds?
If it's a small set, you can make an excel template for each of them in the Excel Importer module. You can then process the data to make it ready for export, and export it using the Excel Exporter module.
If it's a large set of customers and it's not feasible to make templates for each of them, it's going to get a bit more tricky. You could build some kind of functionality that guides the users through making their own excel template before uploading their file, maybe.