Before you can clean Magento cache you need to now what are you cleaning.
- Configuration - All configuration is kept in XML files and database table core_config_data. Data from these files and table is collected, merged and saved in the cache.
- Layouts - Layouts are XML instructions of blocks combinations.
- Blocks HTML Output - Caches HTML output from blocks and dynamic data generated in block classes will be cached too.
- Translations - Translations are collected and merged from locale files and core_translate database table.
- PEAR Channels and Packages - This feature is presently not in use since introduction of MagentoConnect Manager.
- Collections Data - If enabled, Magento internal object collections will be cached according to specific cache id logic for each collection.
- Catalog - In this section, checkboxes are used not to enable, but to refresh cache contents.
- Refresh Catalog Rewrites - Re-generates SEO friendly URLs for catalog links (products and categories)
- Clear Images Cache - cleans auto-generated resized and watermarked catalog images.
- Refresh Layered Navigation Indices - Re-generates index for catalog layered navigation
Now that you now all the things you can refresh, click on System => Cache Management, then check Cache types that you want to refresh. After that you need to click in the Actions box, select refresh option and click on "Submit" button.
After that you need to click "Flush Magento Cache" and "Flush Cache Storage" buttons.
"Flush Cache Storage" Removes all files and directories from the /var/cache directory.