It seems that auto focus is not your problem... any camera lens has a minimum focus distance which is related also to the focal length. In your kit lens the minimum focal distance seems to be 25cm at 18mm so if you are in auto mode it will start blinking to highlight that you are out of focus. In Manual you are still out of focus but the camera will let you take the photo :).
If you need to go very close to an object you may need a macro lens, or close up filter which are cheaper! Enjoy your camera and give us some more stories!