I have a D5000 - the big brother to the D3000. It's perfectly fine for photographing pens.
Without examples, it's difficult to diagnose your problem, but my suspicions are:
1. The most likely issue is lighting. You don't have to spend anything to correct this problem - just walk around the house. Look for a north-facing window with nothing to obstruct light from the sky on the outside (shrubbery, outbuidings, trees, etc). Put a table in front of that window. Ideally, you want a neutral top on the table - an old blanket is fine. Solid colors - NO PATTERNS. Nicely finished wood is ok, but be careful that the wood texture doesn't detract attention from the object you are photographing, and you want to avoid a high-gloss finish that will create glare. Turn the on-camera flash OFF, and use only light coming through the window. Carefully note how the shadows fall around the object you are photographing - they should fall toward you in front of the object, and away from the window. Now, get a sheet of white paper and hold it in front of the object to reflect some of the light back into those shadows. You don't want the shadows to disappear entirely, but you do want to lessen their intensity in front of the object.
2. Framing - get your camera as close to the object (pen) as you can, and fill the frame with the image. This is very important for two reasons. First, you are photographing the pen, not the table and the window. Second, if you get close and fill the frame, the camera will adjust the exposure for the pen and the lighting described above. If you are too far back, you will only get a silhouette, but if you get close, you will be able to see the texture in the wood in the pen. The 'kit lens' on the D3000 will allow you to zoom close enough to fill the frame with the pen. Also, shoot from the front, not down from the top.
3. Exposure. Put the camera into A (aperture preferred mode), and adjust it for a small aperture (ie, a high f number). That will result in maximum depth of field (sharpness from front to back in the image). It will also mean that the camera will use a long shutter speed. The kit lens that comes with the D3000 has image stabilization - make sure it's turned on. Hold the camera as steadily as you can to avoid any movement.
4. Practice - the more practice you get, the better the images will be.
