Thousands of files and folders can’t just be cut and pasted into SharePoint; you need a plan and a tool to make it happen.
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Hi Sos2,
Looking for a solution to Thousands of file and folders just try PCVITA File Share to SharePoint Migration application which can easily and smoothly Migrate files Share including Folders, Document, Content, library, PPT, Word, Excel into SharePoint Server 2010, 2007 & 2003 without any misplace of your files.
read more : http://www.pcvita.com/file-system-to-sharepoint.html