Most of the Union and Confederate dead were buried in a series of mass graves scattered across the battlefield. When the war ended, the Union bodies were moved to a newly created cemetery (what is now the Shiloh National Cemetery), but the federal government refused to allow the Confederate dead to be removed from the burial trenches. There are five known trenches, with at least two others located somewhere in the park. The largest is located near White Oaks Pond and it contains the remains of over seven hundred Confederates. It is at this spot that the Stars and Bars are flown.
I'm heading to Shiloh next Wednesday, and I'll take and post a picture of this.