TkMedit consists of two windows. The top window, called the Display Window, shows the currently displayed slice. Multiple panes can show multiple orientations and configurations. The bottom window, called the Tools Window, contains the controls and feedback information.

Information about the currently displayed data can be obtained by moving the mouse over the Display window or by clicking to set the cursor. As the mouse is moved in the display window, the Mouseover section of the Tools window will display information about the voxel (or volume element) under the tip of the mouse arrow. Alternatively, most tools set the cursor upon clicking with the left button. The Cursor section of the Tools window displays information about the voxel under the cursor. By default, the cursor is drawn as a red cross. Guidelines are drawn on the sides of the Display Window to help locate the cursor.

It is possible to display multiple orientations of data simultaneously in the Display Window. This is done by splitting the window up into multiple viewing panes, each with a different slice, orientation, or other viewing characteristics. The cursor can be linked between so that a click in one pane to set the cursor will update the cursor in all the other panes. There are three built-in configurations: Single View, Multiple Views, and Mosaic View. These can be activated by clicking on the appropriate icon in the Navigation Toolbar ( attachment:Icons/TkMedit/icon_view_single.gif Single, attachment:Icons/TkMedit/icon_view_multiple.gif Multiple, attachment:Icons/TkMedit/icon_view_mosaic.gif Mosaic) or by choosing the appropriate item in the View menu.

In the latter two views, there is more than one pane in the Display Window. A green border is drawn around the active pane. To make another pane active, click in it to set the cursor. The Mouseover section of the Tools Window will only display information about the voxel under the mouse if it is in the active pane.