T3550 Capillary Electrophoresis (CE) chip

One simple but very effective way to clean a microchip is to flush an alkaline solution through the channels. A solution of 1 M sodium hydroxide in water works well, but a lower concentration might also be sufficient. If traces of the cleaning solution remain inside the chip after cleaning, rinse with water or ammonia. Further, plastic parts should not be exposed to alkaline solutions.
To remove particulate matter from your chip, a water bath with ultrasonic agitation can be used, preferably while flushing a watery solution through the channels.
Glass microchips can be heated (e.g. 400°C) causing any organic material on the glass surface to degrade. Try to use lower temperatures first because burning the content could make it stick. Make sure you only heat the glass chip and not the plastic parts around it.
Concentrated sulfuric acid works well to dissolve organic material, such as fibres, that are difficult to remove with alkaline solutions. Always keep in mind that you are working with extremely corrosive material. Please note that this instruction is focused on the chip itself, PEEK elements like connectors are not so compatible with strong sulforic acid.
Please note that chips that were coated by Micronit have different guidelines for cleaning!

Wet etched structures are extremely smooth and have a roughness in Angstrom range. The structures are fully optical transparent. 
Large roughness for structures in glass chips is typical observed for structures manufactured by use of laser assisted manufacturing techniques or abrasion-based techniques like powder blasting. Almost all catalogue products from Micronit are manufactured using wet etching to create full transparent channels without substantial roughness.