You need to make adjustments on both frontend and backend codes.
On frontend you can edit the catalog/product/view/options.phtml file. Around line 115 (magento 1.8), you will see:
$$('body .product-custom-option').each(function(element){
In this loop the code goes through all available options in this product, and you can tell to ignore it by exiting the function. But the order of process is the order of options in the product (as it is set in the backend).
After you care sattisfied with the result on the frontend you will have to do the same thing in the backend before the product is added to the cart. You will have to overwrite this file: app\code\core\Mage\Catalog\Model\Product\Type\Abstract.php, inside the _prepareProduct() method, around lines 361 - 367
TODO: Learn moar coding.
– scrollup May 25 '14 at 13:12