You could use C# code like:
FileStream fs = new FileStream(FileSaveName, FileMode.OpenOrCreate); // FileSaveName is FileName to save to
BinaryWriter writer = new BinaryWriter(fs);
writer.Write(Base64EncodedSting, 0, Base64EncodedStringLength); //Base64EncodedSting is Base64Encoded data in XSD element
// writer.Write(Base64EncodedSting); will work also
writer.Close();
fs.Close();
As far as I know, can you put this in a Expression Shape or in a Custom Pipeline.