Whenever you wish to clear any large area of trees, you must ensure you are in compliance with both state and federal laws. When an endangered species is involved, compliance becomes even more important, and more laws are implicated. You may still be able to cut down the trees, but it will likely be more time consuming and more expensive to obtain the required clearances and permissions.
Many states have passed various acts regulating logging and deforestation; the first thing to do before clearing these trees is obtain information on the laws particular to your jurisdiction. For example, in Washington, the Forest Practices Act (PA), found in RCW 76.09, regulates "any activity conducted on or directly pertaining to forest land and relating to growing, harvesting or processing timber."
Under this act, there are four different classes of forest with details on what practices are involved with each. Class 1 practices involve growing and cutting trees, such as Christmas tree growth, as well as removal of less than 5000 board-feet of timber to use personally. Class II forest practices have a small potential for damaging public resources. Class III practices include any activities that require a hydraulic project approval because they are too close to water or wetlands. Finally, Class IV forests are those where logging activity may have a substantial impact on the environment, such as forests designated as critical habitats for endangered wildlife.
If the area where you wish to take down timber is considered a Class IV forest, you would need to obtain a permit from the Department of Development and Environmental Services. To obtain a permit, you would generally need to create a long-term management plan for the forest, along with a variety of other requirements.
These regulations are, of course, specific to Washington, and each state may have its own forest act and its own specifics about when a permit is required to cut trees and what must be done to obtain a permit when necessary.
In addition to state regulations, you must comply with all federal laws including the Endangered Species Act of 1973. Under the Endangered Species Act, any project or action that will result in a "taking" of endangered or threatened species must be approved and you must obtain a permit from the U.S. Fish and Wildlife Service.
A "taking" is defined as harassing, harming, pursuing, hunting, shooting, wounding, killing, trapping, capturing or collecting endangered species. Cutting down large areas of the habitat of an endangered species may be considered to be a "taking," as it is a form of harm and may thus result in the need to obtain a permit.
Obtaining a permit is not impossible, as what's know as incidental take permits are issued to private entities who wish to proceed with construction or other actions that unintentionally impact endangered species.
In order to obtain an incidental take permit, you must submit an application to the United States Fish and Wildlife Service. Your application must include a Habitat Conservation Plan (HCP) which clearly outlines: 1) the impact on the endangered species that your deforestation would cause, 2) any steps you have taken to minimize or lessen the impact of the incidental taking, 3) how you are funding the project and the habitat conservation plan, and 4) any other options you considered but did not choose in order to try to minimize the impact on the endangered animal. Remember that the HCP is a legally binding contract, and you must comply with the terms and obligations outlined in the plan if your permit is granted.
The Fish and Wildlife Service may also include specific "terms and conditions" within the plan, including a "no surprises" clause. This clause is designed to ensure that private landowners will not be required to commit more land or money to a conservation plan than outlined in the permit, even if something unexpected occurs, without the consent of the landowner.