Manual + this forum + CC’s class + LT’s videos will help dispel much of the confusion. I’ve had my AF3 for 5 months and still have lots to learn, but at the same time I do feel somewhat comfortable with it.
 
As for "deleting" scenes... I don't get why you would need to or want to do that... but In Axe Edit you CAN simply erase the name of the Scene.
I DO get not needing 8 (or sometimes even 4) for a given preset, and not wanting to "waste" switches on your footswitch. Here is a little tip that I do...

Make use of PER PRESET FC layouts (I'm assuming you got an FC 6 or 12 - if not... ignore this.) On my FC if one song has 4 scenes labeled INTRO, VERSE, CHORUS, SOLO, on another song I might only need 2 scenes labeled MAIN and SOLO. On that preset I set the LED rings on the unused scene switches to off and put a custom label on that switch as just a "." (It won't allow a blank - and I wish it would.) Then when I look down - I only have 2 switches lit up to choose from. On the next song, I might have 4 or even 5 again. It's per preset that way - and it gives you the same outcome at your feet as "deleting scenes".

I like my FC to be as clean and minimal as possible on stage. Only those buttons that I would need for a given song are lit up and the rest are dark. It changes a little song by song, but with custom colors it makes it super easy for me to see exactly what I need to hit with my foot for any given moment.

If you are a "guitar to amp" guy with little to no FX, or maybe only a few and prefer the stompbox world, you can setup your FC to do that too. You don't have to ever use or even see scenes. Just use a stompbox layout or a preset layout on the FC. But I'd bet a steak dinner that once you get to playing with them you will love them. They are probably the #1 feature (to me) that makes this thing so powerful and awesome.

Scenes do exactly what I used to do with a GCX switcher - turn certain FX on or off and change amp channels all with a single button press. No more tap dancing.
 
As for "deleting" scenes... I don't get why you would need to or want to do that... but In Axe Edit you CAN simply erase the name of the Scene.
I DO get not needing 8 (or sometimes even 4) for a given preset, and not wanting to "waste" switches on your footswitch. Here is a little tip that I do...

Make use of PER PRESET FC layouts (I'm assuming you got an FC 6 or 12 - if not... ignore this.) On my FC if one song has 4 scenes labeled INTRO, VERSE, CHORUS, SOLO, on another song I might only need 2 scenes labeled MAIN and SOLO. On that preset I set the LED rings on the unused scene switches to off and put a custom label on that switch as just a "." (It won't allow a blank - and I wish it would.) Then when I look down - I only have 2 switches lit up to choose from. On the next song, I might have 4 or even 5 again. It's per preset that way - and it gives you the same outcome at your feet as "deleting scenes".

I like my FC to be as clean and minimal as possible on stage. Only those buttons that I would need for a given song are lit up and the rest are dark. It changes a little song by song, but with custom colors it makes it super easy for me to see exactly what I need to hit with my foot for any given moment.

If you are a "guitar to amp" guy with little to no FX, or maybe only a few and prefer the stompbox world, you can setup your FC to do that too. You don't have to ever use or even see scenes. Just use a stompbox layout or a preset layout on the FC. But I'd bet a steak dinner that once you get to playing with them you will love them. They are probably the #1 feature (to me) that makes this thing so powerful and awesome.

Scenes do exactly what I used to do with a GCX switcher - turn certain FX on or off and change amp channels all with a single button press. No more tap dancing.
All good advice. My presets vary depending on the purpose (song-specific or 'kitchen sink'), and I have yet to use more than 3 scenes in a song-specific preset. I also have all my song-specific presets duplicated with all 'scenes' being accessible via a single controller pedal, which is divvied up into 2 or 3 'regions' using a trick I picked up from @NDESMAREST mid last year that lets you get 3 sounds on one pedal. This trick makes it so even just one FC6 is bordering in overkill, and I have two. The kitchen sink presets usually end up using all 12 buttons, though.... :)
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Also, don't forget the release notes as they mention/describe all the awesome updates from Cliff and team. Also, wiki has all the updates in spreadsheet format that has helped me numerous times trying to remember various changes that may not have made it to the PDF manual until updated. I love the fact that you can book mark and label various posts and threads for easy reference when needed.
 
This is probably beating a dead horse at this point, and I'm sorry if it is, but just delete the name of the Scene. Yeah, it doesn't delete anything inside the scene, but if you're using an FC, front screen, or the drop down that lists the scenes in Axe Edit, you won't see something that looks like a viable scene. I've had my Axe3 for a week. I watched videos for almost a year before pulling the trigger, mostly because I was originally going to go for the FM3, but then got Trumpbux. Its slightly off the original topic, but in my week of ownership, the biggest thing I can say about scenes, presets, and channels is make sure you are on the correct channel you want before selecting a new amp or otherwise and hitting that save button. Oh, and use scene controllers if you want to tweak settings on your devices between scenes. Super powerful, and there are vids on it if you need help.
 
I set up bookmarks in my toolbar to the following pages. Can't recommend each of them enough. These plus Leon Todd Videos will make you a master quickly. I am pretty quick on the uptake with computers, electronics, and audio gear. It took about 2 weeks for me to learn all I needed to learn and build my perfect kitchen sink preset including layout tweaking on the FC12, trying every preset out, running all the cables I needed and all the other typical set up stuff. Now I play much more than I tweak. But I do still tweak and learn new things. I still have things to learn about all the effects types and controllers. There's so so much depth to make whatever you want with it. That's why its a best in class guitar product used by some of the worlds biggest bands including Metallica who for example have enough money to have any gear in the world.

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https://forum.fractalaudio.com/
https://wiki.fractalaudio.com/wiki/index.php?title=Category:Axe-Fx3
https://www.dropbox.com/s/8fvjvrqnryihp86/Yeks_Guide_to_the_Fractal_Audio_Amp_Models.pdf
https://www.dropbox.com/s/h9ncef0pk4frp62/Yeks_Guide_to_the_Fractal_Audio_Drive_Models.pdf
https://www.fractalaudio.com/downloads/manuals/axe-fx-3/Axe-Fx-III-Owners-Manual.pdf
https://www.fractalaudio.com/downloads/manuals/FC-X/FC6+12-Owners-Manual.pdf
https://www.fractalaudio.com/downlo.../Fractal-Audio-Footswitch-Functions-Guide.pdf

The AxeFX can be as simple as you want but it can also be complex enough to do anything you can imagine short of playing the the guitar for you. Then again... there's a looper in there too...
 
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