If the target creature is affected by any effects that modify its power or toughness without setting them to specific values (such as from Giant Growth), Omnibian’s effect will be applied before those effects. In the example given, the creature will be 6/6.

If the target creature has any counters on it that modify its power and toughness (such as a +1/+1 counter), those counters will continue to affect the creature after it becomes 3/3. In the example given, it will be 4/4.

This effect changes only the power, toughness, and creature type of the targeted creature. It does not cause that creature to lose any abilities.