Sometimes a unit will only be partially in cover (ie some of the models are in or behind cover and some of them are out in the open). In this situation the owning player has to remove casualties from amongst the models in the open first until there are none left – they are the more obvious targets and will suffer commensurately.
Units Partially in Cover
Source: Core Rulebook 3E, p. 55
When only some of a unit's models are in cover, casualties must be removed from the models in the open first.