Ionogram scaling is the process of reconstructing electron density with respect to height by using the measurements of a remote sensing instrument known as ionosonde. In this study, a novel two stage ionogram scaling technique, ISED, is proposed. In the first stage, Hidden Markov Models (HMMs) are used to identify the actual ionospheric reflections in the ionosonde measurements. In the second stage, an IRI-Plas model based optimization problem is solved to obtain the vertical profile that generates the best least squares fit to the reflections identified in the first stage. To show the performance of ISED in global scale, experiments are conducted on 14,812 ionograms recorded at the three different stations which are Pruhonice in Czech Republic, Eielson in USA and Sao Luis in Brazil. Application of ISED to raw ionograms indicate 97.6% of the cases, ISED provides accurate electron density reconstructions, which is an improvement about 8.7% over ARTIST, most commonly used ionogram scaling technique.