This thesis outlines the relevance of fluorinated compounds in organic chemistry, more specifically in different scaffolds of fluorophores and the applications reported as well as highlighting the potential for different applications of the selected compounds in the first chapter. The second chapter describes the synthesis, characterization, optical, and physicochemical properties of a series of fluorinated squaraine dyes and highlights their potential in biological applications. The chemical structure of synthesized compounds was characterized using ¹H and ¹⁹F nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS). Biological distribution studies and further imaging studies were conducted following the full characterization of compounds.