You can see that the exposed surface of the last/youngest agate layer tend to look bumpy/bubbly/kidneylike and that is due to the radiating structure of the quartz microscrystals that make up each layer of the agate. The layers are kind of like "growth rings" which the fibers of each layer tend to be oriented to each other.  Think of a phantom quartz crystal with each layer of dirt outlining each crystal growth ring. The phantom quartz crystal grew in steps without any distortions, and it may be the same thing with the agates.

     The silica crystallizes in form of radiating needles/fibers. In most agates, the radiating needles are too small to be seen with naked eyes, but some agates like this Union Road agate pictured below contain the agate crystals large enough to be noticable (easier to seen in hand than those pictures).  The radiating structure can be also noted in some thin agate slabs held in front of a light source.

Note faint fiber-like texture on 
the weathered broken surface of agate