Here I am writing down the steps to remove shortcut menu from all the sugarcrm modules.

Step:1 Open you header.php file which you can found under /sugarcrm/themes/sugar/header.php (I am using Sugar as my default theme) then you can comment the following lines

foreach($module_menu as $menu_item)
{
$subModuleCheck = 0;
$subModuleCheckArray = array("Tasks", "Calls", "Meetings", "Notes","Prospects");           if(isset($menu_item[3]))
{
If(in_array($menu_item[3], $subModuleCheckArray) && (array_key_exists("Calendar", $modListHeader) ||array_key_exists("Activities", $modListHeader))) $subModuleCheck = 1;
}
if(!isset($menu_item[3])|| !isset($modListHeader) || (isset($menu_item[3]) && (key_exists($menu_item[3],$modListHeader) || $subModuleCheck)))
{
$after_this = current($module_menu);
if ($menu_item[1] != 'Deleted Items') {

$xtpl->assign("URL", $menu_item[0]);
$xtpl->assign("LABEL", $menu_item[1]);
$xtpl->assign("SC_MODULE_NAME", $menu_item[2]);
$xtpl->assign("SC_IMAGE", get_image($image_path.$menu_item[2],"alt='".$menu_item[1]."'  border='0' align='absmiddle'"));

if (empty($after_this)) $xtpl->assign("SEPARATOR", "");
else $xtpl->assign("SEPARATOR", "
");
else {
$xtpl->assign("DELETED_ITEMS_URL", $menu_item[0]);
$xtpl->assign("DELETED_ITEMS_LABEL", $menu_item[1]);
}
$xtpl->parse("main.hide");
$xtpl->parse("main.left_form.sub_menu.sub_menu_item");
}
}
$xtpl->parse("main.left_form.sub_menu");
$xtpl->assign("SHORTCUTS", $app_strings['LBL_SHORTCUTS']);

Step 2. Then you have to open your header.html file which you sugarcrm/themes/sugar/header.html after that you have to comment these lines

{SHORTCUTS}