To have an empty table:
set(handles.mytable,'data',cell(nrows,2))
If you already have data in the first two columns that you want to keep while deleting the third col:
mydata = get(handles.mytable,'data');
newdata = mydata(:,1:2);
set(handles.mytable,'data',newdata)
Replace handles.mytable with the handle to your table in the gui.
