Best way to achieve this is to make one field to hold all the choices or checkboxes. Use the field type Checkbox (Multiple). Then use the layout described below:
Open your field that is capturing all the available selections (choices). At the bottom of the field screen, on the left bottom side of the field, look for the parameters Cols. and Rows. Set the Cols to 3 and the rows to 34 (need this many rows to equal at least 100 field selections, or 3x34 = 102 selections). Add all your single fields into this single field and add the options or choices at the bottom of the field setup page.
This should get you to what you were asking about. If I am understanding what you were wanting to do. It also will layout on both registration form and profile page nicely.
Scott