A microwave plasma assisted reactor comprising: (a) a first microwave chamber having a reference plane at a reference axial location Z 0, extending in an axial direction z > Z 0, and having a circular cross section with a radius R1(z) that varies as a function of the axial position z, wherein the first microwave chamber comprises: (i) a first waveguide portion positioned adjacent the reference axial location Z 0, (ii) a second waveguide portion positioned adjacent the first waveguide portion such that the first waveguide portion is positioned between the second waveguide portion and the reference axial location Z 0, where the radius R1(z) of the first microwave chamber in the first waveguide portion is less than the radius R1(z) of the first microwave chamber in the second waveguide portion; (iii) a third waveguide portion (120, 220) positioned adjacent the second waveguide portion such that the second waveguide portion is positioned between the third waveguide portion and the first waveguide portion, where the radius R1(z) of the first microwave chamber in the third waveguide portion is less than the radius R1(z) of the first microwave chamber in the second waveguide portion; (iv) an electromagnetic wave source; and (v) an upper conducting sliding short in electrical contact with the third waveguide portion (120, 220) and disposed in an upper portion of the third waveguide portion (120, 220) at an axial distance L s above Z 0, the upper conducting sliding short having a central opening and defining an upper boundary of the first microwave chamber; wherein at least one of the first waveguide portion and the third waveguide portion comprises a cylindrical waveguide section with the radius R1(z) as a constant value in the cylindrical waveguide section; (b) a plasma chamber having an outer wall, the plasma chamber extending into the first waveguide portion of the first microwave chamber such that at least a portion of the plasma chamber is located at z > Z 0; and (c) a conductive stage having a reference surface extending into the plasma chamber. (a) a first microwave chamber having a reference plane at a reference axial location Z 0, extending in an axial direction z > Z 0, and having a circular cross section with a radius R1(z) that varies as a function of the axial position z, wherein the first microwave chamber comprises: (i) a first waveguide portion positioned adjacent the reference axial location Z 0, (ii) a second waveguide portion positioned adjacent the first waveguide portion such that the first waveguide portion is positioned between the second waveguide portion and the reference axial location Z 0, where the radius R1(z) of the first microwave chamber in the first waveguide portion is less than the radius R1(z) of the first microwave chamber in the second waveguide portion; (iii) a third waveguide portion (120, 220) positioned adjacent the second waveguide portion such that the second waveguide portion is positioned between the third waveguide portion and the first waveguide portion, where the radius R1(z) of the first microwave chamber in the third waveguide portion is less than the radius R1(z) of the first microwave chamber in the second waveguide portion; (iv) an electromagnetic wave source; and (v) an upper conducting sliding short in electrical contact with the third waveguide portion (120, 220) and disposed in an upper portion of the third waveguide portion (120, 220) at an axial distance L s above Z 0, the upper conducting sliding short having a central opening and defining an upper boundary of the first microwave chamber; wherein at least one of the first waveguide portion and the third waveguide portion comprises a cylindrical waveguide section with the radius R1(z) as a constant value in the cylindrical waveguide section; (i) a first waveguide portion positioned adjacent the reference axial location Z 0, (ii) a second waveguide portion positioned adjacent the first waveguide portion such that the first waveguide portion is positioned between the second waveguide portion and the reference axial location Z 0, where the radius R1(z) of the first microwave chamber in the first waveguide portion is less than the radius R1(z) of the first microwave chamber in the second waveguide portion; (iii) a third waveguide portion (120, 220) positioned adjacent the second waveguide portion such that the second waveguide portion is positioned between the third waveguide portion and the first waveguide portion, where the radius R1(z) of the first microwave chamber in the third waveguide portion is less than the radius R1(z) of the first microwave chamber in the second waveguide portion; (iv) an electromagnetic wave source; and (v) an upper conducting sliding short in electrical contact with the third waveguide portion (120, 220) and disposed in an upper portion of the third waveguide portion (120, 220) at an axial distance L s above Z 0, the upper conducting sliding short having a central opening and defining an upper boundary of the first microwave chamber; (b) a plasma chamber having an outer wall, the plasma chamber extending into the first waveguide portion of the first microwave chamber such that at least a portion of the plasma chamber is located at z > Z 0; and (c) a conductive stage having a reference surface extending into the plasma chamber.