I think you can use conditional mapping for this:
The following example will only map properties with source and destination type decimal. You can define your mapping like this:
Mapper.CreateMap<Source, Destination>()
.ForAllMembers(s=>s.Condition(t =>t.SourceType == typeof(decimal)
&& t.DestinationType == typeof(decimal)));
And then use the mapping like this:
var src = new Source();
src.Obj1 = 1;
src.Obj2 = 2;
src.Obj3 = 3;
var dst = Mapper.Map<Destination>(src);
The dst variable will now have only the Obj1 and Obj2 properties mapped. Obj3 is 0 (default value of an int).
Not sure if this is exactly what you mean. Maybe you only want to check source property type or destination property type, but i hope you get the point.
The above is a generic approach which will still work if more properties / types are getting added to the classes.