Not only is science based medicine proven to work, the side effects, risks, interactions and contradictions are well established. This is not the case with 'alternative' medicine.
If certain science based medicines are found to be unsafe or problematic, they are withdrawn or otherwise dealt with, as science is self correcting. This is not the case with 'alternative' medicine.
Science based medicines are standardized and controlled. This is not the case with 'alternative' medicine. Herbal drugs for example, vary in quality and quantity of active chemical ingredient, some have been found to be contaminated with heavy metals and other toxins. They are typically handed out by people with little or no medical training.
'Alternative' medicine is rife with scams and quackery, like detox foot baths, acai berries, crystal healing and the preposterous and ludicrous homeopathy. This is not the case with science based medicine.
'Alternative' medicine proponents resort to conspiracy theories and personal attacks when pressed for evidence of efficacy (as can be seen here). This is not the case with science based medicine.
The US National Center for Complimentary and Alternative Medicine (NCCAM) have spent 2.5 Billion Dollars and 10 Years studying 'alternative' medicine, only to find that most work no better than placebos: http://www.msnbc.msn.com/id/31190909
We have a name for 'alternative' medicine that works - 'medicine'.
Always seek the evidence.
EDIT: Sudhakar - it is disingenuous to say Doctors are the third leading cause of death in the US. Firstly the figure varies depending on where you read it, secondly it refers to medical errors - so mistakes made not only by doctors but by anyone in the medical/hospital system, thirdly you fail to mention the hundreds of millions of lives that are improved or saved each year, and finally I seriously doubt that you can prove that one single person's life has ever been saved by alternative medicine. You only have anecdotes.