oh my, we've all been there. There's more than one way to do this. I usually create a new layer below the one they are on (to be deleted later), select just the top layer of everything you can see and group them. Then move it to the layer below. Hide that layer. you can then delete everything else.
Now, if you're not sure you've gotten everything selected the first time around (because I'm never sure), you can always create 3 or 4 new layers, select the top objects, hit group and move the selection to a new layer, hide the layer. then when everything is on it's own layer and you're sure that you have a complete set of it, then delete the 3 layers you don't want.