Mindanao of southern Philippines is a case in point where there are observed systematic efforts by entities, often connected to or with influence by national government and interventionists from western states, who are promoting a certain version of Islam and trying to influence the so-called government-mainstreamed madaris to be exemplars of this “disinfected” and “desirable” Islam. This desirable Islam is a “tamed Islam”, conveniently labeled and described as “moderate” and “democratic”, an appropriated concept largely based on a doctrine designed by the think-tanks of the Bush government and US neo-conservatives guided by intellectual and scholarly works such as the RAND policy papers. In the guise of advancing democratic and libertarian ideals, these documents that inform State security policies have unwittingly harmed and prejudiced certain concepts and practices among Muslims as “potentially terroristic”, which is unfair and not based on solid knowledge of Islam as a comprehensive belief system and a way of life. Neither are these considerate of deep lived-experiences of community-inspirited and culturally-embedded Muslim life. It is common knowledge that the Philippine educational system is patterned after the American system. In fact, in its present free-market- oriented values and elitist utilitarian ideals, the Philippine educational system has been one of the enduring vestiges of American colonial influence. It is an important institution in the forefront of promoting the neo-liberal ideas that advances US hegemonic and militarist interests in the Philippines and south east Asia. Before the 9/11 and the Bush War against Terrorism, in Mindanao provinces and villages where Muslims are dominant, community-based madaris, albeit independently, have been existing side-by-side and harmoniously with the public school system as well as private religious sectarian schools operated by other faith communities, mostly Christian, and Bangsamoro parents have the choice of sending their children to either schools or a complementation of both. Then, so-called “terrorist schools” did not exist. Today, where the Bangsamoro teachers and parents have, for their own best reasons and interests, chosen not to have their community madrasa to be mainstreamed, it has become a common practice for military establishment to “invite” the asatidh and ulama for regular appearance at their command base or stations for security briefings, “proper monitoring” and to periodically confirm the religious intellectuals’ non-association and non-involvement with so-called “terrorist schools” or extremist groups. This counter-terrorism measures are clear forms of intimidation and harassment, to say the least. Indeed, in many cases where Muslims are minorities, Islamic scholarship have been suffering from the impact of Islamophobia mostly coming from the western world, that comes in subtle and not too subtle forms of Counter Terrorism Measures of governments. In the Philippines, for instance, the discussion of Jihad, is discouraged and deleted from the vocabulary of government-mainstreamed madaris. By way of further illustration, it is also important to mention that among the victims of the infamous Camp Bicutan massacre of Bangsamoro political prisoners in February 2006 were Muslim religious and scholars many of whom were cases of mistaken identity and apprehended on mere hear-say and rumor of affiliation with religious extremism. To date, there remains languishing in jail a number of young asatidh and ulama who were suspected as members of the Abu Sayyaf Group. The increasing incidents of summary executions and extra-judicial killings of ulama and asatidh are also indications of this silently creeping yet unabated campaign to denigrate Islam and to stigmatize Islamic scholarship in the Philippines, which has risen to the point of it becoming a systematic political persecution of Bangsamoro religious scholars.