SuperUser Hal_Al addresses this issue very well:
Nondividend distributions do not go anywhere on your actual tax return. Box 3 is for your information. Box 3 is a "return of capital". That is, you have been given back part of your original investment. As such, you reduce you cost basis, by the box 3 amount, in your own records, for when this investment (typically stock or mutual fund) is sold in the future.
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