When using manual focus you have to adjust the plane of focus using the focus ring to acquire correct focus. You will have to choose this yourself and if I understand you correctly you have not done this. Of course there is a slight chance that the lens will already be set to focus at the depth you want but they are slim indeed. Using a wide aperture will make this even less likely since a wide aperture will give you a very small depth of field.

I know you are using a Nikon 3300 and are probably using the 18-55 mm kit lens too (if you're using something else they will work similarly anyway), but the following image shows the Canon counterpart. Their construction is very similar however. The lens has two rings, one for zooming and one to adjust focus manually.

To set the focus manually either look through the viewfinder or use live-view and then turn the manual focus ring of your lens (make sure to set it in manual focus mode first since you might damage the auto focus gear if you turn it otherwise). You will see that some areas blur out and others come into focus. This is a result of you moving the plane of focus of the lens. Make sure that whatever you intend to have in focus is and take the picture.

Please note that shooting as manually as possible when starting out doesn't necessarily give you the most educational experience. It might be better to familiarise yourself with the camera first and then introduce the more advanced features one at a time. Especially auto-focus is something that is very handy and manual focus is best used in special purpose photography such as macro and astrophotograpy.