The clear command has the ability to be used only to clear renamed items: /clear @p minecraft:stone 0 5 {display:{Name:Best}} will not clear regular stone blocks, but will clear stone blocks named "Best". However, the clear command will fail if the item name in the brackets contains a space: /clear minecraft:stone 0 5 {display:{Name:The Best}} will not work. As shown in the included image, the space in the item name cuts off the end of the command.
The command will also fail when the Name tag is put in quotation marks. {display:{Name:"The Best"}} will claim that the string parsing fails due to an unbalance quotation as opposed to a bracket.