Super Mario Maker is confirmed to not support 3D, with it only playing in 2D.
The box art for Super Mario Maker for Nintendo 3DS has been revealed and confirms the game does not support the handheld’s 3D feature – it only plays in 2D. Nintendo previously confirmed that the upcoming port won’t allow players to share courses online, nor does it have all the available tools in the original Wii U version. Super Mario Maker for Nintendo 3DS is scheduled to launch on December 2.
Source: My Nintendo News