Islam wasn't forced on Bosnians or Albanians, neither was it limited to those regions. Conversion to Islam in the Balkans was (with some very limited exceptions, like the devşirme) an entirely voluntary process. It "was minimal during the fourteenth and early fifteenth centuries, increased slightly in the late 1400s, and rose steadily throughout the sixteenth century. It appears that the process peaked in the mid-1600s only to slow down and come to an almost complete stop by the end of the 1700s."^1

Bosnia and Albania took different paths toward conversion to Islam. Bosnia converted very quickly and was majority Muslim by the end of the sixteenth century, while Albania only began to rapidly convert during the late seventeenth century. Major urban centers across the Balkans were mostly Muslim during the sixteenth and seventeenth centuries. Dennis Hupchick estimates that 12.5% of the Bulgarian population was Muslim around 1600, and that percentage greatly increased over the course of the seventeenth century.^2 Bruce McGowan, citing Bulgarian historian Nikolai Todorov, notes that by the 1830s the population of the Ottoman Balkans was 33-42% Muslim.^3 This obviously included plenty of Muslims living outside of Bosnia and Albania. For instance Southern Bulgaria, Macedonia, and the Dobruja region also contained huge Muslim populations, constituting local majorities.

So what happened to them? The answer is that as the Ottoman Empire lost control of territory, the Muslim population either fled or was ethnically cleansed. The first major instance of this was in the late seventeenth century. Cities like Buda and Pecs had been majority Muslim, but their populations were either massacred or fled following the advance of the Habsburgs into Hungary. The Muslims of Serbia largely fled once that country gained autonomy in 1830, moving instead to Kosovo and Macedonia. Many of the Muslims of Bulgaria likewise fled once independence was achieved, as between 1880 and 1945 574,000 of them left the country,^4 a number roughly equal to the current Muslim population of Bulgaria, which still represents about 8% of the country today. Hundreds of thousands more were forced to assimilate or flee during the 1980s as the state adopted repressive measures against them. The Muslims of Greece were forcibly transferred to Turkey by mutual agreement between the two countries in 1923, uprooting some 500,000 people. Bosnia as well has a much lower percentage of Muslims today than it did in the past, a result of flight, persecution, and genocide.

So the answer to your question is that Muslim communities did exist throughout the Balkans, but they were mostly destroyed over the course of the nineteenth and twentieth centuries.

1. Tijana Krstic, Contested Conversions to Islam: Narratives of Religious Change in the Early Modern Ottoman Empire, (Stanford University Press, 2011), pp. 20-1.
2. Dennis Hupchick, "The Social Position of the Bulgarians ," in The Bulgarians in the Seventeenth Century, (1993). [Unfortunately I don't have a page number, I just noted that it's in this chapter]
3. Bruce McGowan, Economic Life in Ottoman Europe: Taxation, Trade, and the Struggle for Land, 1600-1800, (Cambridge: Cambridge University Press, 1981) 85.
4. Antonina Zhelyazkova, "Islamization in the Balkans as a Historiographical Problem: The Southeast-European Perspective," in Fikret Adanir and Suraiya Faroqhi, eds. The Ottomans and the Balkans: A Discussion of Historiography, (Brill, 2002), pp. 235-6.