I believe this is something that has to do with the items being stored in the ItemsControl, not ElementFlow itself. You shouldn't need to modify ElementFlow in order to achieve this, as this functionality really has nothing to do with ElementFlow's
logic at all.
The way ElementFlow displays your items into 3D is to paint a 3D rectangle with a visual brush, which uses your item's view (painted via its data template) as source.
Therefore, of course you can change the data template so that your items are rendered differently -- and they'll show up differently in the 3D model. You're most likely using bindings and triggers to do this.
However, you need a way to tell whether the data template whether an item is the currently selected one. Your item object probably won't have this property -- not every object has an IsSelected property for this use. Therefore, there is no way
for you to determine in your data template whether that particular item is the currently selected one.
One idea I have is to bind to the ElementFlow control's SelectedItem property -- which always returns the currently selected item. In your data template, put in a trigger that activates when the SelectedItem is the same as the data context --
at that time, the item would be the selected one.