This is a copy of the flow chart from the BSI standard and it details how arboricultural input should be included at the various stages of the site development (in an ideal world) process.
While the standard itself carries no legal power, it can be and is, used by local planning authorities as a reference to conditions to be met, in order for planning permission to be granted. It is also being used as a requirement in order to validate an application (that at least a BS5837 style tree survey be attached to the outline planning application and a full implications assessment be attached to a full application).
Although this flow chart indicates how the design and construction phases of a development should incorporate tree related issues, it has been my experience that it rarely happens this way. This is not necessarily a problem for me, but it often cause headaches for the design team if they've already prepared a design proposal before obtaining arboricultural advice. The implications are potentially huge in terms of cost, time and frustration, if a material consideration is not considered throughout the entire design process, but only as an afterthought when trying to get planning permission.
The BS5837 standard does recommend the below methodology for designing developments near trees. It shows that a tree survey is one of the first requirements in the design process. From the tree survey, a tree constraints plan is developed which identifies areas that are developable and any constraints to the site, through the requirements of trees that need to be retained. Once the design team know what land they have to work with, they are far more likely to produce a design that will require little or no modification at all, to accommodate the retainable trees on the site. This saves time and money, as well as ensuring good quality of service to the client.
The below flow chart is a very good benchmark for efficient use of the time spent by all those in the design, planning and development teams. It's pretty self-explanatory and can be scaled for any size project - large or small. The flow chart is straight out of the BS5837:2005 standard:

BS5837:2005 flow chart showing how arboricultural input is required throughout the development project
The tree survey
The initial tree survey starts everything off as this will determine those trees that should be retained (threreby creating possible site constraints, or even possibly rendering a site undevelopable) and those that can be justifiably removed. The trees are surveyed with the intention of assessing their contribution to their surroundings, their safe useful life expectancy, their form and prominence in the immediate landscape. There are other factors they are assessed on, such as structural integrity etc..
BS5837 provides a cascade chart indicating which level of value should be placed on the trees surveyed. A copy of the cascade chart is below:

BS5837 tree quality cascade chart
All the trees on and around the site should, be surveyed and placed into one of these tree quality categories.
The trees would be plotted on some kind of 2D map, that is dimensionally accurate. It doesn't have to be a CAD based drawing but future drawings are made much easier utilising this computer based application. An example is below:

example BS5837 tree survey plan

example BS5837 tree survey schedule