As drew advised: editing the project file is one way. Another way is to edit the Solution file in a mechanism similar to that of the csproj file.
In a solution file, a project with a specific GUID holds the details of a set of folders.
Write a small app that will read your folder and output a small text of the desired output. Generate new Guids until the file is created. Just paste this at the top of the .sln file. 2150E333-8FDC-42A3-9474-1A3956D46DE8 seems to be the GUID used for Solution Items.
This sample has a few subfolders with content in a nested structure.
i.e.
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "NewFolder1", "NewFolder1", "{4CDFCC66-45BD-4B6D-8758-FEF7E9F61C1C}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "SubFolder1", "SubFolder1", "{771BDBFB-5C01-4C51-A170-D88ECA8DE896}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "SubFolder2", "SubFolder2", "{5D23AB90-5EF6-4611-A575-34F7B50BB1B6}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "NewFolder2", "NewFolder2", "{135E9F67-2DF8-4458-AC6D-FF82FC1B3BC6}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "SubSubFolder1", "SubSubFolder1", "{B41C7BAA-7E3D-405B-96AB-005120D12D26}"
ProjectSection(SolutionItems) = preProject
NewFolder1\SubFolder1\SubSubFolder1\a.txt = NewFolder1\SubFolder1\SubSubFolder1\a.txt
EndProjectSection
EndProject