Deposition temperature effect on morphological, topological and magnetic characteristics of nanoparticle-assembled Co50Fe50 films produced by femtosecond pulsed laser deposition (fs-PLD) on Kapton substrate was investigated. For substrate temperature T-s >= 550 K, a decrement of the nanoparticle's aggregates and an increment of the nanoparticle's density were observed with respect to room temperature deposition; this in association with a strong increase of the magnetoelastic anisotropy energy lead to a reduction of the remanence ratio, a significant rise of the saturation and coercive fields and an enhancement of the saturation magnetization. The results are discussed focusing on: i) the correlation between films structure and their magnetic behavior; ii) the role of the different anisotropy energies in determining the harder in-plane magnetic behavior for T-s >= 550 K. The thermal strain of Kapton substrate holds an important role in generating morphological and topological characteristics of the fs-PLD films and corresponding magnetic properties. (C) 2011 Elsevier B.V. All rights reserved.