create the html in the loop, assigning it to a variable. Then at the end of the loop, append it.
for (var i = 1; i<=question_per_block; i++){
var html = '<tr>';
for (var j = 1; j<=no_of_td; j++){
html += '<td>';
for (var k = 1; k<=choice_per_question; k++){
html += '<input type="checkbox">';
};
html += '</td>';
};
html += '</tr>';
// now that the html table row is built, append it
$('#ans_set_table').append(html);
};