Price is set at simple product level in Magento 2 (and configurable products will inherit the special price from simple products beneath it).

The quickest way to do it correctly would be to use the REST API inside a script.  This is the best way if you're a beginner - Magento has created this as an interface for external integration which should be used wherever possible.

http://devdocs.magento.com/swagger/index_20.html#!/catalogProductRepositoryV1

The correct endpoint is catalogProductRepository's PUT /V1/products/{sku} - 

Note that you need to put the storeview code into the calling URL as described here.

http://devdocs.magento.com/guides/v2.0/rest/rest_endpoints.html

Otherwise if you have a test environment and are more confident with coding you can create your own script to update a lot quicker:

Inside a class you'd have:
    protected $action;
    public function __construct(\Magento\Catalog\Model\Product\Action $productAction) {
       $this->action = $productAction;
    }

    public function updatePrice($productId, $storeId, $data) {
        $this->action->updateAttributes($productId, $data, $storeId);
    }

then to run it use the following;

     $specialPrice = ''; //or null, can't remember off the top of my head which clears it - perhaps either.

     $data = ['special_price' => $specialPrice];
     $storeId = 1; //whatever store id you like
     $productIds = [1,2,3,4,5,6,7]; //whatever product ids you wish to change.

     $this->updatePrice($productIds, $data, $storeId);

run for each store.

Apologies for any mistakes, I am just typing by memory.  Please run on a test environment first!