I usually filter my Fluent NHibernate models overriding the DefaultAutomappingConfiguration:
public class AutoMappingConfig : DefaultAutomappingConfiguration
{
public override bool ShouldMap(Type type)
{
return typeof(EntityBase).IsAssignableFrom(type);
}
}
And tell Fluent NHibernate about it:
Fluently.Configure()
.Database(databaseConfig)
.Mappings(
m =>
m.AutoMappings.Add(
AutoMap.AssemblyOf<User>(new AutoMappingConfig()));