SELECT 
  cscart_product_filters.filter_id, 
  cscart_product_features.feature_id 
FROM 
  cscart_product_features 
  LEFT JOIN cscart_product_filters ON cscart_product_filters.feature_id = cscart_product_features.feature_id 
WHERE 
  cscart_product_features.feature_type = 'E' 
  AND cscart_product_filters.seo_enabled = 'Y'

Query time 0.00018

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_filters ALL feature_id 10 Using where
1 SIMPLE cscart_product_features eq_ref PRIMARY PRIMARY 3 hobilifedt.cscart_product_filters.feature_id 1 Using where

Result

filter_id feature_id
10 18
316 550