It's common to extract properties common to all (or most) of your entities into a base-class. Sometimes you may want your base-class to be an open generic type, with which each inheritor can change the generic argument for different behaviour.

An example of this is using a single generic argument to dictate the Id type.

public abstract class BaseEntity<T>  
{  
  public T Id { get; private set; }  
}

When using this kind of base-class, you just need to ignore it like any other base type.

AutoMap.AssemblyOf<Entity>()
  .IgnoreBase(typeof(BaseEntity<>));

You just need to remember to use the unbound type definition for it to apply to all subclasses (BaseEntity<> instead of BaseEntity<int>).