Serpentine channel / Microreactor, 140x250µm, 500mm length

Absolutely! Micronit is a key supplier for flow cells in the Next Generation Sequencing market and can manufacture flow cells competely according to your specific requirements.  What can be customized?

The channel shape. The channel height and width.
For wet etching its important to consider that channel height and minimal channel width are related.
{minimal channel width} = 2 * {etch depth} + {initial mask opening, typcial 5-10µm} 
Larger aspect ratios (relation between channel depth and width) are possible using dry etching. For this, a glass/silicon combination is most common. Choice of material. For instance, fused silica is a good option when UV light is used. Schott D263 bio can be a good alternative for some specific fluorescent labels.  Surface flatness. We can provide ultra flat surfaces.

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.