Extracting portions of an image

Brandon,

As I (mis)understand it, you wish to have the red parts showing, with the background structure, and get rid of the grey parts.

Presuming the red parts are vector artwork (paths including Compound Paths) at a reduced Opacity (so you can see the background structure through it), and the background structure is a raster image, you may:

1) Select all the red paths, but not the background (you may select everything, then ShiftClick the background object to deselect it), then Ctrl/Cmd+8 (Object>Compound Path>Make);

2) Ctrl/Cmd+C+B;

3) ShiftClick the background image and Ctrl/Cmd+8 (Object>Clipping Mask>Make);

You may:

4) Select everything and Ctrl/Cmd+G to Group.

This should give you the desired appearance, but with the all outlying/inlying invisible parts of the raster image still selectable.

If you wish to get rid of the raster image parts that are outside the area with the red parts, you may go on from 3) with the dirty destructive deed as follows:

4) In the Transparency palette/panel dropdown list select anything but Normal (Multiply is fine; this step may be unneeded in your version, you may try without it);

5) Object>Flatten Transparency, just keep the defaults including 100% Vector;

6) Shudder (optional, unless unavoidable).

This will crop everything to the Bounding Box of the Clipping Path, so that only what is inside that Bounding Box will still be there and selectable.

You may (still):

7) Select everything and Ctrl/Cmd+G to Group.