I am answering my own questions, as some may get directed here.
I had solved this according to @mkl suggestion. After observing the result of getYScale() in PDFStreamEngine.java, I have come to a conclusion that the size of superscript was less than 8.9663. so I had kept a condition in the PDFStreamEngine.java before creating a TextPosition, which will be processed by PDFTextStripper.java. The code is below:
if(textXctm.getYScale()>=8.9663) {
processTextPosition(
new TextPosition(
pageRotation,
pageWidth,
pageHeight,
textMatrixStart,
endXPosition,
endYPosition,
totalVerticalDisplacementDisp,
widthText,
spaceWidthDisp,
c,
codePoints,
font,
fontSizeText,
(int)(fontSizeText * textMatrix.getXScale())
));
}
Let me know if my approach has any flaws in eliminating only the superscripts. Thanks.