Communication via diffusion (CvD) is an effective and energy efficient method for transmitting information in nanonetworks. In this work, we focus on a diffusion-based communication system where the reception process is an absorption via receptors. Whenever a molecule hits to the receiver it is removed from the environment. This kind of reception process is called first passage process and it is more complicated compared to diffusion process only. In 3-D environments, obtaining analytical solution for hitting time distribution for realistic cases is complicated, hence we develop an end-to-end simulator for he diffusion-based communication system that sends consecutive symbols. In CvD, each symbol is modulated and demodulated in a time slot called symbol duration, however the long tail distribution of hitting time is the main challenge that affects the symbol detection error. The molecules arriving in the following slots become an interference source when detection takes place. End-to-end simulator enables us to analyze the effect of inter symbol interference (ISI) without making any assumptions on the ISI. We propose an ISI cancellation technique that utilizes decision feedback for compensating the effect of previously demodulated symbol. Three different modulation types are considered with pulse, square, and cosine carrier waves. In case of constraints on transmitter or receiver node it may not be possible to use pulse as a carrier, and peak-to-average messenger molecule metric is defined for this purpose. Results show that, the proposed ISI mitigation technique improves the symbol detection performance and the amplitude-based modulations are improved more than frequency-based modulations.