You have 3 ways to remove an item from the store:
Go to Configure -> Menu-> Select the item.
Under "Unavailable in" select from a scroll down menu the specific store that you want the item to be removed.
Go to Configure ->Locations-> Select the location.
Uncheck the item from the menu (on the right side of the page, under the locations picture).
Go to Configure -> Locations -> Select the location.
Select the item under the POS Items Permanently / Temporarily Unavailable bar.
You'd have to type the item's name and then choose from a scroll down menu.
You can select multiple items easily this way: