The difference between 2D and 3D MID is that the latter supports 3D secure transactions.
The 3D secure authentication is an additional fraud prevention scheme to process transactions. It allows customers to create and assign a password to their card that is then verified whenever a transaction is processed through a site that supports the use of the scheme. The addition of password protection allows extra security on transactions that are processed online. The scheme is a collective of Verified by VISA (VBV) and MasterCard Secure Code (MSC).