The generated BEM mesh is stored on disk as a set of three files: an element file, a coordinate file, and an information file. All three mesh files have the same base name, with the file extension specifying the file type. The file extensions are .bee for the element file, .bec for the coordinate file and .bei for the information file. All the files are ASCII text files for easier processing and portability.

The information file (.bei) defines the high level properties of the mesh. Each mesh consist of one or more boundaries. Since the boundaries separate tissues, each boundary has an inside and outside tissue type. The first row of the information file contains information about the mesh structure. The entries of the first row are the number of boundaries, the number of nodes, the number of elements, and the number of nodes per element respectively. For linear meshes there are 3 nodes per element and for quadratic meshes there are 6 nodes per element. The following rows of the information file define the boundary information. Since an element can be a part of only one boundary, the elements of the mesh are grouped according to the boundary, and from outside to inside. Therefore, each boundary is a consecutive group of elements. For the boundary rows, the first column is the boundary index. Second column gives the number of elements in the boundary. The third and fourth columns represent the inner and outer tissue class of the boundary.

The tissue class is an integer representing a tissue. This number is defined per mesh, there is no global assignment of tissue classes at the moment. The purpose of tissue class is to uniquely define the various tissues that are represented by the mesh. Since different tissues may have same or similar conductivities, using a tissue class identifier provides a better distinction. Furthermore, this scheme makes it possible to solve the same mesh geometry using different tissue conductivity values.

The coordinate file (.bec) defines the physical coordinates of the nodes in the BEM mesh. There is one node per row. The first column is the node index, and runs from one to the number of nodes in the mesh. The next three columns represent the x, y, and z coordinates of the node.

The element file (.bee) defines the connectivity of the nodes for each element. The element file defines one element per row. The first column is the element index, and runs from one to the number of elements in the mesh. The next three (linear mesh) or six (quadratic mesh) columns define the node indexes for the element. Note that the order of nodes are important, and define the orientation of the element.