The effect of the length of fluoroalkyl substituents on the refractive index (n) and glass transition temperature (T$_{g}$) of methyl methacrylate (MMA)-fluoroalkyl methacrylate (FAMA) copolymers (poly(MMA/FAMA)) was investigated. The copolymers were solution-polymerised in order to prepare cladding materials for plastic optical fiber (POF). The copolymer composition, T$_{g}$, and refractive index (n) of the copolymers were determined using $^1$H-NMR spectroscopy, differential scanning calorimeter, and prism coupler, respectively. As the length of fluoroalkyl units in FAMA and the content of FAMA in poly (MMA/FAMA) increased, the T$_{g}$ and n decreased monotonically. This indicates that although the copolymerization of MMA and FAMA is effective in controlling the n of cladding materials, the decrease in T$_{g}$, is inevitable. The interfacial instability between PMMA and MMA-trifluoroethyl methacrylate (TFEMA) copolymers, observed during annealing at 17$0^{circ}C$, was greater at higher TFEMA contents. The observation was interpreted in terms of the solubility parameter concept combined with the Flory-Huggins interaction parameter.rameter.