MyCustomPersistenceModel.cs

using System.Reflection;
using FluentNHibernate.AutoMap;
using FluentNHibernate.Framework;
using MyApplication.Core.Domain;

namespace MyApplication.Core.Persistence
{
    public class MyCustomPersistenceModel : AutoPersistenceModel
    {
        public MyCustomPersistenceModel()
        {
            AddEntityAssembly(Assembly.GetAssembly(typeof(ValueObject<>)))
                .WithConvention(c =>
                {
                    c.IsBaseType = type => IsBaseType(type);
                })
                .Where(t => t.Namespace == "MyApplication.Core.Domain" && IsBaseType(type.BaseType));
        }

        private bool IsBaseType(Type type)
        {
          return type == typeof(Entity) || type == typeof(ValueObject<>);  
        }
    }
}