Bibliometrics and citation analysis have become an important set of methods for library and information science, as well as an exceptional source of information and knowledge for many other areas. Their main sources are citation indices, which are bibliographic databases like Web of Science, Scopus, Google Scholar, etc. However, bibliographical databases lack perfection and standardization. There are several software tools that perform useful information management and bibliometric analysis importing data from them. A comparison has been carried out to identify which of them perform certain pre-processing tasks. Usually, they are not strong enough to detect all the duplications, mistakes, misspellings and variant names, leaving to the user the tedious and time-consuming task of correcting the data. Furthermore, some of them do not import datasets from different citation indices, but mainly from Web of Science (WoS). A new software tool, called STICCI.eu (Software Tool for Improving and Converting Citation Indices-enhancing uniformity), which is freely available online, has been created to solve these problems. STICCI.eu is able to do conversions between bibliographical citation formats (WoS, Scopus, CSV, BibTex, RIS), correct the usual mistakes appearing in those databases, detect duplications, misspellings, etc., identify and transform the full or abbreviated titles of the journals, homogenize toponymical names of countries and relevant cities or regions and list the processed data in terms of the most cited authors, journals, references, etc.