Magento – How to select the images as base image thumbnail image in bulk

Go to System->Store management, click on the name of the store view you want to remove and you should see a Delete button on the top right corner. That should delete your store view. There is an intermediary page that asks you if you want to back-ul the store before deleting it. I suggest to back up your entire database before starting anything, then just skip that step.
[EDIT]
You can only delete the store views that are not used as default in their store groups.
so you should edit the store group, and change the default store view for it.
Same goes for store groups. You cannot delete one that are default in their website.

Here is given programmatically adding media images to product, you can adjust this code to your own importing script:

    $mediaGalleryAttribute = Mage::getModel('catalog/resource_eav_attribute')
        ->loadByCode(Mage_Catalog_Model_Product::ENTITY, 'media_gallery');
    $mediaGallery          = $mediaGalleryAttribute->getBackend();
    $attrCode              = $mediaGalleryAttribute->getAttributeCode();


    $product          = Mage::getModel('catalog/product')->load($productId);
    $mediaGalleryData = $product->getData($attrCode);
    /**
     * If you want to remove old images use this code
     */
    if (isset($mediaGalleryData['images'])) {
        foreach ($mediaGalleryData['images'] as &$image) {
            $image['removed'] = 1;
        }
        $product->setData($attrCode, $mediaGalleryData);
    }
    /**
     * Here is real image file path
     */
    $thumbnailFile = 'real/path/to/thumbnail/file.jpg';
    $imageFile     = 'real/path/to/image/file.jpg';
    try {
        //Set thumbnail
        $imageFileUri = $mediaGallery->addImage($product, $thumbnailFile, null, false, false);
        $mediaGallery->setMediaAttribute($product, 'thumbnail', $imageFileUri);

        //Set image (or base image, small image whatever you want
        $imageFileUri = $mediaGallery->addImage($product, $imageFile, null, false, false);
        $mediaGallery->setMediaAttribute($product, 'image', $imageFileUri);
        $product->save();
    } catch (Exception $e) {
        Mage::logException($e);
    }