Saxophone repairman Matt Stohrer of http://www.StohrerMusic.com shows one way to cleanly patch a hole left from a neck pickup. Neck pickups were semi-commonly installed- by drilling a hole in the neck- in the 1970s and 1980s. Nowadays mics do the job pretty well, and most folks with a neck pickup installed would like to remove them since they can be prone to leakage, devalue the horn compared to a decently done patch, and (to some, including myself) look quite unsightly.
This is how I do it, and might not be the best way, but hopefully can provide you with more information on the subject than you had prior to watching.
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Also check out the Open Source Saxophone Project: http://www.OpenSourceSaxophoneProject.com