Most of the core modules that make use of the DNN FileSystem include in their SQL stored proceedures that get an object or collection of objects a join between the column which stores the file link (in the form of "fileid=23") and the DNN core Files table so that an actual or relative file path can be returned.  You can also obtain a FileInfo object which includes the Filename, Folder, etc. by way of the FileController class:

Dim fctrlr As New DotNetNuke.Services.FileSystem.FileController
Dim finfo As DotNetNuke.Services.FileSystem.FileInfo = fctrlr.GetFileById(FileId, PortalId)
Dim relativeFilepath As String = System.IO.Path.Combine(fi.Folder, fi.FileName)

Note that you also have to supply the PortalId to the GetFileById method.