When automating the infusion altar from thaumcraft, you might run into some issues. The altar has somewhat special item handling, that won't let you slap AE right onto it. Getting the items into the right spots, with AE support, and then starting the infusion all have their own hurdles. Even returning the finished item can be a little difficult do to the structure having no clear distinction between in/out slots.
For this task we do have a lot of options. OC, sfm, any pipe + redstone, as well as intense variation in these setups. Below are some explanation of how to go about using each, as well as their strengths and faults. As usual there isn't a clear winner, and you can do it any way you please, but sometimes it's difficult to find even one that will work.
However there are a few things that seem universal. The infusion claw from gadomancy is integral to starting infusions properly. It will consume some wand vis, and take a small startup time, afterwards the infusion will begin. This is redstone controlled, and used to begin every infusion.
Next are WAs. Somehow somewhat of a controversial topic, however these are a godsend for infusions. When provided with 6A of tier, and screwdriver'd they will accelerate the infusion alter when placed adjacent to the matrix. Some infusions can take upwards of a minute, which makes this a must for lategame crafting.
Sfm is one of the easiest options. No lua, and no complex redstone. The setup is fairly simple here you will mostly be using commands to see if certain pedestals are full or not, and using this to preform 2 discreet actions.
If you wish to skip reading about it, here is a visual tutorial explaining the same concept: https://youtu.be/tVfvpJW3U80
Cable and AE setup
You will want to touch every pedestal with inventory cables, as well as placing a redstone emitter next to the claw. Also connect to the AE input chests. Place an AE interface on it, on blocking mode. A pattern will consist of all the items needed, minus the essentias. The item that goes in the middle chest needs to be the first in the pattern, or any position you keep constant. Make sure you have an infusion provider from thaum AE, or another large essentia source. This by default won't check essentia values, so make sure you have a lot, or make a system for that.
The commands for this will be very simple. We simply want to define 2 states the altar can be in. If there are no items in any of the pedestals, that means it's free to craft more. If there's only an item in the middle and nowhere else, that means it is finished and you can pull your output.
To do this we setup an item condition. That will check if your middle pedestal is full. Then connect the true output to checking if your other pedestals have any items. On a true output from the 2nd condition, we know it's full, and this can be left unconnected. Our false when checking the remaining pedestals can be connected to an input from the middle pedestal, to an output into AE. This means only the middle has an item, signifying crafting is complete. The final option, the main pedestals being empty, we connect to a condition checking the AE input chests. Once again simply check for any items, and use the true output here to connect to an input. Connect this to an input from the AE chest, and then into an output specifically for the middle pedestal. This will ensure the first item will end up there. Then connect that to another output that lists all the other pedestals. This will move all the items, and keep the middle item in the right spot. Then add a redstone emitter command at the end, which will trigger the claw to start the infusion.