I am making graphs for a scientific publication. They must be submitted as EPS vector graphics. The graphics program that I'm using can output a vector based PDF. I have made an artboard the exact size of the image requirements, and I select the graph from the PDF and bring it into AI. Everything I want to include in the graph is on the artboard. However, when I upload the eps files to the rendering program (to get proofs), the stuff outside of the artboard is also visible. I tried doing alt-eraser and making a marquee of the stuff I don't want, but it won't delete. I tried making a rectangle the size of the artboard, aligning it to the artboard, Pathfinder/Crop, but that hides stuff in my original graph. I'm a beginner with AI, and I'm not sure what else to try. I tried to attach an EPS file, but am unable.
Finally found the answer: Here it is. If you want to totally eliminate content outside a mask in Illustrator (giving you a true crop), you can use the following method:
Select the path that you would have used for the clipping mask and, instead of making a mask, fill it with, oh, say, white. Then, set the opacity for that masking object to 0% using the transparency palette/panel. Then, with that object and the underlying raster image selected, flatten transparency. (Use 100% vector on the quality slider and make sure the 'Preserve alpha channel' option is unchecked.) Ungroup the result.
You should now be able to independently select the various portions (inside and outside the mask) and discard those you don't need. The links palette/panel will show you what's going on.
You can use this method with multiple clipping masks in a single operation. You don't even have to initially embed the underlying image for this to work.