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You can go ahead and prune off anything that did not sprout, but I would leave the main pruning for when the tree is dormant. You could pinch some new growth if you wanted, or snip a few live twigs, but much better to wait.

If you want the tree to grow up and out, and not have so much leaf mass in its lower area this will take time. Prune to shape some main branches, but do not remove much of the lower growth yet. The lower growth is protecting the bark from sunburn. Each year you can take off a little bit of the lower growth to show off the trunk. The top will eventually get wide enough to provide the shade. Similarly, do not thin the upper branches all in one go. Do this also over several years to minimize sun burn.

If you want to keep it about the size it is then prune more heavily, especially the longest branches. This would turn it into a 'lollipop on a stick'. Not a nice way to prune a Japanese Maple.

Suggest you google Acer palmatum and look at images of how others have been pruned.
 

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Mentha requenii is also called Corsican Mint, Jewel Mint of Corsica.
Stays pretty much flat.
Has VERY SMALL purple flowers. Almost need a hand lens to see them.
GREAT fragrance.
Wonderful planted in part shade around stepping stones. Where it gets stepped on it won't grow (so is pruned to stay off the stones by foot traffic) and crushing it releases the great scent.

Similar looking plants:
Soleirolia soleirolii, Baby Tears. Older botanical name Helxine.
Full shade.
There is a golden leafed one and a variegated one.
No fragrance, flowers even smaller.
This one is occasionally kept as a house plant, and is common in Bonsai as a ground cover.
Can get about 6" tall in a mild, damp setting.

Pratia pedunculata with lots of older names, the most commonly known is Isotoma. Blue Star Creeper. Full sun down to about half a day of sun, but won't flower in complete shade. Flowers to 1/4", almost white (Alba) to sky blue (original species), and there is a selection with richer colored flowers (County Park), somewhere between blue and lavender. Leaves are not quite a round as the other 2.

There are other ground covers with similar small round leaves, but these are the big 3, most common in the milder zones. (I am in USDA zone 9b and do most of my landscape design work in nearby zones)
 

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Do not use 'pruning paint' or other sealant on pruning cuts.
When properly pruned these cuts will heal by themselves.
Pruning paint often does harm.

This information is over 30 years old, but companies that sell stuff (like pruning paint) still want their money, so keep on pushing it.
Like certain aquarium keeping myths, this one keeps on going, too.

http://puyallup.wsu.edu/~linda chalker-scott/Horticultural Myths_files/Myths/Wound sealer.pdf

http://homeorchard.ucdavis.edu/8057.pdf

And more info about Japanese Maples and related plants.
http://www.ipm.ucdavis.edu/PMG/GARDEN/PLANTS/maple.html
 
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