If you have a brick and mortar store, you can set certain items to only be sold in store and not be visible to be sold on your website.  To do this, we have to modify the reserved quantity. This is found when you edit a product and go to a tab called Variant Info.  
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Note, setting the reserved quantity will also affect the quantity numbers in your POS and other sales channels (eBay, Amazon and TCGplayer).

The reserved quantity tells your admin how much of a quantity you want to keep in your store/admin/inventory, allowing you to keep some quantity of a product to be sold in store.

For example:

If you have 10 quantity of a product, and you set your reserved quantity to 0, that will enable you to sell all 10 quantities of that product (as you are reserving 0). 

If you have 10 quantity of a product, and you set your reserved quantity to 5, that will enable you to sell up to 5 quantities of that product (as you are reserving 5), meaning once you have sold 5 quantities of this product, it will be hidden from the site afterwards so that you can sell the remaining 5 only in store.

If you have 10 quantity of a product, and you set your reserved quantity to 10, as your reserved quantity is now the same (or in other cases it could be higher) then this will cause your product to not appear on your website but you would still be able to sell all 10 of those products in your store.

For information on how to batch update your product's reserve quantity, please see this link.