Why does InDesign files create multiple boxes the size of the document when exporting as a PDF?

Question

Sometimes I need to place customer-supplied files into Illustrator templates to prepare for printing. If they have been originally created in InDesign and I need to make some adjustments in the file, I cannot isolate individual elements in the file. If I try to delete the box, half of the whole design may be deleted.

Answer 1

This is an answer I posted to a similar question. The context isn't InDesign, but the kernel of the issue is the same: clipping masks. There are any number of recipes for producing PDF's and most of them result in a stack of media-sized clipping masks, or so that's how they parse when opened in Illustrator.
PDF's output from drafting packages and other "foreign" sources, when opened for editing in Illustrator, quite often contain clipping masks and compound paths based on component associations that Illustrator (and its users) wouldn't typically make or recognize. Your drawing will come into Illustrator behaving like one big group that won't ungroup. That's because it isn't a group; it's a clipping mask based on the extents of the drawing. The first thing I do is select all, (Ctrl+A), then release clipping mask, (Ctrl+Alt+7). Pressing (Ctrl+Alt+7) repeatedly often reveals that there are other clipping masks nested within the large outer one. Most of the time, you can release all the masks this way without changing the appearance of anything. Each released mask usually leaves behind an invisible frame. (no stroke or fill), that you can delete or leave, depending on how intensive your editing will be. The release of nested masks may also result in groups and sub-groups that I also like to release similarly by pressing Ctrl+A then Ctrl+Shift+G repeatedly. Once you've done this, you should be able to select and treat any of the individual components on the artboard as desired, although you may still run into some compound path items that will hinder your selection process. These can also be released, but you'll want to be more cautious with respect to how it might alter appearances, especially if there are filled paths involved.