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The safest method to avoid killing your turf grass is hand pulling Johnsongrass. You can also apply vinegar for a safer herbicide, but it will still burn your lawn if it gets on it.

There are organic herbicide options that will kill grass but not flowers, including white vinegar or a dish soap solution. Commercial selective herbicides can also target grass over other plants, but read the instructions carefully to avoid damaging your garden. Herbicides that kill grass but not flowers usually include ingredients like clethodim and sethoxydim. Otherwise, your best bet will be to weed by hand.

Several tools exist that can help remove unwanted grass. The one you choose depends greatly on how much you need to remove and how hard you'd like to work. A sod or turf cutter is the fastest method while using a shovel is labor-intensive and much slower. You may also need a garden rake, tiller, and wheelbarrow. 

It’s not legal to intentionally damage a neighbor’s tree. Even if the roots of a tree encroach into your yard, if you damage or kill a tree that belongs to your neighbor, you can be held liable for the damage in most cases. Since herbicides can spread through the tree, causing damage to the whole tree and not just the roots that are on your side of the property line, you shouldn’t poison your neighbor’s tree. The other downside to this method is that if the tree dies, it can fall onto your property and cause more damage, so herbicides are best avoided in this circumstance.