Functional nanocoatings of hollow-core microstructured optical fibers (HC-MOFs) have extended the domain of their applications to biosensing and photochemistry. However, novel modalities typically come with increased optical losses since a significant surface roughness of functional layers gives rise to additional light scattering, restricting the performance of functionalization. Here, the technique that enables a biocompatible and removable nanocoating of HC-MOFs with low surface roughness is presented. The initial functional film is formed by a layer-by-layer assembly of bovine serum albumin (BSA) and tannic acid (TA). The alkaline etching at pH 9 results in the reduction of surface roughness from 26 nm to 3 nm and decreases fiber optical losses by three times. The nanocoating can be fully removed within 7 min of the treatment. Natural biocompatibility of BSA alongside antibacterial and antifouling properties of TA makes the presented nanocoating promising for biophotonic applications.