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There are 3 main reasons against laser treatment for Genital warts

Persistent HPV After Laser Treatment

Persistent infection after laser treatment is documented and it is recommended to get HPV testing after laser treatment to make sure it has been eradicated. Please refer to National Institute of Health link below to read the study.

http://www.ncbi.nlm.nih.gov/pubmed/18714574

HPV Transmission By Laser

Laser plume has been shown to actually transmit disease (HPV). Laser is used by various medical specialties to vaporize, ablate, or cut tissue. Laser emits light energy in the lower infrared range (10 600 nm), which is absorbed by water. Because of the relatively high water content of tissue, significant amounts of plume are generated. Human Papilloma Virus exist (survive) in this plum. Please refer to Following link of Journal of American Medical Association:

http://archderm.jamanetwork.com/article.aspx?articleid=479032

Laser Treatment with high relapse rate

Laser intensity and depth of penetration is pre set. This is the reason that many patients with laser therapy have high relapse rate of recurrence of genital warts. The warts comes in different shapes and thickness and hardness and they don’t follow the exact pattern. We have seen many patients in our institution with genital warts recurrence after laser treatment. In many instances laser will not eliminate the warts.
It is very important to remember that genital warts is not skin tag, mole or fibro epithelial that you burn and cook the sticking out tissue and it goes away easily and never grow back. Human papillomavirus will reproduce the genital warts after it falls off again and again because of human Papilloma virus.

Final

For past decade or so laser has gotten attention in practicing medicine.  The name of the laser is accompanied with the thought of something high-tech miracle that could fix anything. However the reality is somewhat different. Laser is usually a single wavelength amplified beam of light radiation. There has been many manufacture and different type and name on the laser such as diode, CO2, ... but it all comes to one easy understanding conclusion:

Think about a powerful beam of light that burns.