It is likely that nearby milfoil will simply spread into the area just cleared as it is more aggressive than the native plants so repeated weeding will be required. Dredging or digging is possible but completely disrupts the lake bottom and suspends sediments. Often milfoil will come back unless you have deepened the area beyond the reach of sunlight. Another form of control would be covering the lake bottom with mats. This creates a sterile environment where no plants could grow, and it is very expensive.
Some lakes draw down the water level in the winter to freeze the roots.
This is very hard on the fish that move into the small areas of the deep holes. The smaller fish have nowhere to hide from the larger fish and are eaten. In Lincoln Pond the milfoil infestation became much worse after a draw down as this was the most aggressive plant to return. It took over the whole lake bottom where the sediments had been exposed. Biological control seems to be a bright light on the horizon.