The serialization sample demonstrates using Dotfuscator in an application that makes use of serialized objects that must be exchanged with non-obfuscated code. If your obfuscated application is the only producer or consumer of the serialized objects, then this sample does not apply.
Serialization must be considered when using Dotfuscator because all of the provided serialization formatters embed type and field information in the persisted data stream. The implication of this is that classes and fields that are serialized must be excluded from renaming, otherwise it would be impossible to de-serialize objects persisted with non-obfuscated code. Since method definitions are not persisted, they do not need to be excluded from renaming.
The serialization sample demonstrates how to configure Dotfuscator to selectively exclude types and fields from renaming. Instructions are included for using both the command line and the graphical interface.